{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where devstage_curation_coarse = \"Multi-stage\" and tissue_curation = \"Trunk\"", "rows": [[26016, "SRR25868588", "SRX21589851", "SRS18767424", "SRP457982", "PRJNA1011844", "Comparison of zebrafish toxicity among different developmental windows of exposure to three environmentally relevant PFAS compounds", "PRJNA1011844", "Other", "The per and polyfluoroalkyl substances PFAS are of significant global concern due to their highly ubiquitous and persistent nature  bioaccumulation in organisms  and potential toxicity. The aquatic environment is known as an important sink for PFAS resulting in high concentrations in aquatic organisms. However  little is known about the developmental windows of sensitivity in which the PFAS chemicals are biologically active  in addition to the toxicity endpoints that best reflect chemical hazard. In this study  zebrafish Danio rerio were exposed to a 0.33% DMSO vehicle control  1uM chlorpyrifos CAS 2921 88 2 positive control  and eight concentrations 0 100 uM  half log dilutions of three environmentally relevant PFAS compounds in concentration response: PFOS CAS 1763 21 1  PFOA CAS 45285 51 6  and PFHxS CAS 355 46 4. There was also a group of unexposed zebrafish aliquoted from a single pool into all exposure plates to serve as a quality assurance measure. The goal of this study was to generate transcriptomic point of departure tPOD; a benchmark dose/concentration  based treatment level below which a concerted gene expression response is not observed estimates for zebrafish exposed to PFAS compounds as a health protective exposure level for risk assessment. Through the use of short term embryo/larval plate based high throughput toxicity tests  tPODs were determined across seven distinct developmental windows 6 hpf 24 hpf  6 hpf 48 hpf  24 hpf 48 hpf  6 hpf 120 hpf  24 hpf 120 hpf  48 hpf 120 hpf  96 hpf 120 hpf to assess how common experimental design variables e.g.  different exposure durations  exposure at different developmental stages affect point of departure estimates.", null, null, null, null, "T5VAa5", null, "strain:AB wild type|age:24 hpf 120 hpf|dev stage:embryo|collection date:2022|geo loc name:USA: Minnesota  Duluth|sex:not applicable|tissue:whole body zebrafish embryo|biomaterial provider:US EPA Great Lakes Toxicology & Ecology Division  6201 Congdon Blvd  Duluth  MN 55876|breeding method:Adult zebrafish AB wild type strain were housed in an onsite culture facility at the US Environmental Protection Agency USEPA laboratory in Duluth  MN. The fish were raised in a flow through system with control UV treated  filtered Lake Superior water LSW at a flow rate of 250 mL/minute. Fish were held at 26 \u00b1 1\u00b0C under a 16/8 hour light/dark photoperiod cycle. Fish were housed in 5.5 gallon tanks with <100 zebrafish per tank. Adult fish were fed live brine shrimp Artemia nauplii twice daily. The night prior  breeding zebrafish in groups of 4 males x 6 females were separated into breeding tanks containing a plastic screened spawning basket. The next morning  approximately 2 hours post the lights turned on  embryos were collected and maintained in filtered LSW in an incubator set at 28.5\u00b0C. At approximately 4 hpf  zebrafish embryos were screened under a stereo microscope  and only similarly staged embryos were sorted out for chemical exposure. All dead  malformed  and unfertilized eggs were discarded.|collected by:Great Lakes Toxicology & Ecology Division|sample type:Total RNA|time code:5|dose:0|dose units:ug/L|treatment:VehicleControl|replicate ID:rep2|repeat sample:No|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA Seq of danio rerio: whole organism embryo control", "T5VAa5 S217", "T5VAa5 S217", "At the end of each PFAS exposure period  zebrafih embryos were homogenized in Qiagen buffer RLT and betamercaptoethanol  then frozen. RNA was isolated with Ambion MagMAX 96 Total RNA Isolation kit. Samples were transferred to 0.5 mL Eppendorf tubes in prepration for RNA Seq library prepation. RNA was normalized to 6 ng/uL using epMotion 5075. Illumina compatible Lexogen CORALL RNA Seq libraries were then prepared for RNA sequencing. Library pools were quality checked and quantified using a combination of Qubit dsDNA HS  Agilent 4200 TapeStation HS DNA1000 and Invitrogen Collibri Library Quantification qPCR assays by the Michigan State University RTSF Genomics Core. Each pool was loaded onto 1 lane of a NovaSeq S4 flow cell. Sequencing was performed by Michigan State University in a 2x150bp paired end format using a NovaSeq 6000 v1.5 300 cycle reagent kit. Base calling was done by Illumina Real Time Analysis RTA v3.4.4 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP457982", null, null, "T5VAa5_S217_L002_R1_001.fastq.gz T5VAa5_S217_L002_R2_001.fastq.gz", "fastq fastq", 8100529500.0, 27001765.0, "T5VAa5 S217 L002 R1 001.fastq.gz", "0:150 1:150", "A:2094646242;C:1839873833;G:2144213073;T:2021734883;N:61469", 150, 150, null, null, 2094646242, 1839873833, 2144213073, 2021734883, 61469, "SRX21589851", "SRS18767424", "SRA1703738", "U.S. Environmental Protection Agency|Great Lakes Toxicology and Ecology Division", "U.S. Environmental Protection Agency", 2, 0.61505, 0.62102, 0.08204, 0.08402, 0.72581, 0.72545, 0.499, 0.50086, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "lexogen", "bulk", "unknown", "unknown", null, "United States", "2023-09-01", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33164, "SRR29809736", "SRX25309007", "SRS21984115", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "pdx1 morpholino + 20mM STS 5", "GSM8393514", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS|geo loc name:missing|collection date:missing", "pdx1 morpholino + 20mM STS 5", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS", "GSM8393514", "GSM8393514: pdx1 morpholino + 20mM STS 5; Danio rerio; RNA Seq", "GSM8393514 r1", "GSM8393514", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "6_2.fq.gz 6_1.fq.gz", "fastq fastq", 4827420200.0, 24137101.0, "GSM8393514 r1", "0:100 1:100", "A:1278807278;C:1130198430;G:1150325506;T:1268088986;N:0", 100, 100, null, null, 1278807278, 1130198430, 1150325506, 1268088986, 0, "SRX25309007", "SRS21984115", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.9409, 0.94542, 0.08059, 0.07981, 0.69021, 0.68887, 0.47275, 0.47095, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33165, "SRR29809737", "SRX25309006", "SRS21984114", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "pdx1 morpholino + 20mM STS 4", "GSM8393513", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS|geo loc name:missing|collection date:missing", "pdx1 morpholino + 20mM STS 4", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS", "GSM8393513", "GSM8393513: pdx1 morpholino + 20mM STS 4; Danio rerio; RNA Seq", "GSM8393513 r1", "GSM8393513", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "30_2.fq.gz 30_1.fq.gz", "fastq fastq", 4240862400.0, 21204312.0, "GSM8393513 r1", "0:100 1:100", "A:1146088921;C:972830110;G:990127288;T:1131816081;N:0", 100, 100, null, null, 1146088921, 972830110, 990127288, 1131816081, 0, "SRX25309006", "SRS21984114", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.93888, 0.9444, 0.08826, 0.08671, 0.70431, 0.70212, 0.48083, 0.48199, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33166, "SRR29809738", "SRX25309005", "SRS21984113", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "pdx1 morpholino + 20mM STS 3", "GSM8393512", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS|geo loc name:missing|collection date:missing", "pdx1 morpholino + 20mM STS 3", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS", "GSM8393512", "GSM8393512: pdx1 morpholino + 20mM STS 3; Danio rerio; RNA Seq", "GSM8393512 r1", "GSM8393512", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "24_2.fq.gz 24_1.fq.gz", "fastq fastq", 4822516400.0, 24112582.0, "GSM8393512 r1", "0:100 1:100", "A:1276866727;C:1130641795;G:1148897951;T:1266109927;N:0", 100, 100, null, null, 1276866727, 1130641795, 1148897951, 1266109927, 0, "SRX25309005", "SRS21984113", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.94126, 0.94446, 0.07837, 0.07762, 0.6911, 0.69037, 0.46251, 0.4642, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33167, "SRR29809739", "SRX25309004", "SRS21984112", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "pdx1 morpholino + 20mM STS 2", "GSM8393511", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS|geo loc name:missing|collection date:missing", "pdx1 morpholino + 20mM STS 2", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS", "GSM8393511", "GSM8393511: pdx1 morpholino + 20mM STS 2; Danio rerio; RNA Seq", "GSM8393511 r1", "GSM8393511", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "18_2.fq.gz 18_1.fq.gz", "fastq fastq", 4820332000.0, 24101660.0, "GSM8393511 r1", "0:100 1:100", "A:1306037553;C:1103383630;G:1122255994;T:1288654823;N:0", 100, 100, null, null, 1306037553, 1103383630, 1122255994, 1288654823, 0, "SRX25309004", "SRS21984112", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.94035, 0.9445, 0.08468, 0.08417, 0.71106, 0.70897, 0.47897, 0.47969, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33168, "SRR29809740", "SRX25309003", "SRS21984111", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "pdx1 morpholino + 20mM STS 1", "GSM8393510", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS|geo loc name:missing|collection date:missing", "pdx1 morpholino + 20mM STS 1", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:20|agent:STS", "GSM8393510", "GSM8393510: pdx1 morpholino + 20mM STS 1; Danio rerio; RNA Seq", "GSM8393510 r1", "GSM8393510", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "12_1.fq.gz 12_2.fq.gz", "fastq fastq", 4825742600.0, 24128713.0, "GSM8393510 r1", "0:100 1:100", "A:1264457552;C:1145133600;G:1160084092;T:1256067356;N:0", 100, 100, null, null, 1264457552, 1145133600, 1160084092, 1256067356, 0, "SRX25309003", "SRS21984111", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.94613, 0.9501, 0.06915, 0.06812, 0.68941, 0.68852, 0.45659, 0.45507, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33169, "SRR29809741", "SRX25309002", "SRS21984110", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "pdx1 morpholino + 15mM STS 5", "GSM8393509", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS|geo loc name:missing|collection date:missing", "pdx1 morpholino + 15mM STS 5", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS", "GSM8393509", "GSM8393509: pdx1 morpholino + 15mM STS 5; Danio rerio; RNA Seq", "GSM8393509 r1", "GSM8393509", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "5_2.fq.gz 5_1.fq.gz", "fastq fastq", 4816068800.0, 24080344.0, "GSM8393509 r1", "0:100 1:100", "A:1278638535;C:1126555210;G:1141985166;T:1268889889;N:0", 100, 100, null, null, 1278638535, 1126555210, 1141985166, 1268889889, 0, "SRX25309002", "SRS21984110", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.9414, 0.94516, 0.08012, 0.07915, 0.69284, 0.69185, 0.46526, 0.46882, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33170, "SRR29809742", "SRX25309001", "SRS21984109", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "pdx1 morpholino + 15mM STS 4", "GSM8393508", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS|geo loc name:missing|collection date:missing", "pdx1 morpholino + 15mM STS 4", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS", "GSM8393508", "GSM8393508: pdx1 morpholino + 15mM STS 4; Danio rerio; RNA Seq", "GSM8393508 r1", "GSM8393508", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "29_2.fq.gz 29_1.fq.gz", "fastq fastq", 4386218400.0, 21931092.0, "GSM8393508 r1", "0:100 1:100", "A:1181773341;C:1011246416;G:1025789654;T:1167408989;N:0", 100, 100, null, null, 1181773341, 1011246416, 1025789654, 1167408989, 0, "SRX25309001", "SRS21984109", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.94168, 0.94587, 0.08215, 0.08003, 0.69682, 0.69544, 0.47251, 0.47607, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33171, "SRR29809743", "SRX25309000", "SRS21984108", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "pdx1 morpholino + 15mM STS 3", "GSM8393507", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS|geo loc name:missing|collection date:missing", "pdx1 morpholino + 15mM STS 3", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS", "GSM8393507", "GSM8393507: pdx1 morpholino + 15mM STS 3; Danio rerio; RNA Seq", "GSM8393507 r1", "GSM8393507", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "23_2.fq.gz 23_1.fq.gz", "fastq fastq", 4808808800.0, 24044044.0, "GSM8393507 r1", "0:100 1:100", "A:1269564907;C:1132101674;G:1149286214;T:1257856005;N:0", 100, 100, null, null, 1269564907, 1132101674, 1149286214, 1257856005, 0, "SRX25309000", "SRS21984108", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.9434, 0.94774, 0.07109, 0.0703, 0.69264, 0.69183, 0.45908, 0.46455, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33172, "SRR29809744", "SRX25308999", "SRS21984107", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "pdx1 morpholino + 15mM STS 2", "GSM8393506", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS|geo loc name:missing|collection date:missing", "pdx1 morpholino + 15mM STS 2", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS", "GSM8393506", "GSM8393506: pdx1 morpholino + 15mM STS 2; Danio rerio; RNA Seq", "GSM8393506 r1", "GSM8393506", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "17_1.fq.gz 17_2.fq.gz", "fastq fastq", 4805883400.0, 24029417.0, "GSM8393506 r1", "0:100 1:100", "A:1299291748;C:1102517917;G:1122450422;T:1281623313;N:0", 100, 100, null, null, 1299291748, 1102517917, 1122450422, 1281623313, 0, "SRX25308999", "SRS21984107", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.94253, 0.9461, 0.08371, 0.08155, 0.70589, 0.70423, 0.4853, 0.47925, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33173, "SRR29809745", "SRX25308998", "SRS21984106", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "pdx1 morpholino + 15mM STS 1", "GSM8393505", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS|geo loc name:missing|collection date:missing", "pdx1 morpholino + 15mM STS 1", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:15|agent:STS", "GSM8393505", "GSM8393505: pdx1 morpholino + 15mM STS 1; Danio rerio; RNA Seq", "GSM8393505 r1", "GSM8393505", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "11_1.fq.gz 11_2.fq.gz", "fastq fastq", 4812111600.0, 24060558.0, "GSM8393505 r1", "0:100 1:100", "A:1269803704;C:1133657948;G:1150461915;T:1258188033;N:0", 100, 100, null, null, 1269803704, 1133657948, 1150461915, 1258188033, 0, "SRX25308998", "SRS21984106", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.94311, 0.94708, 0.07444, 0.07235, 0.69266, 0.69158, 0.46689, 0.46584, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33174, "SRR29809746", "SRX25308997", "SRS21984105", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "pdx1 morpholino + 0mM STS 5", "GSM8393504", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS|geo loc name:missing|collection date:missing", "pdx1 morpholino + 0mM STS 5", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS", "GSM8393504", "GSM8393504: pdx1 morpholino + 0mM STS 5; Danio rerio; RNA Seq", "GSM8393504 r1", "GSM8393504", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "4_2.fq.gz 4_1.fq.gz", "fastq fastq", 4804978800.0, 24024894.0, "GSM8393504 r1", "0:100 1:100", "A:1266882676;C:1131396187;G:1149418875;T:1257281062;N:0", 100, 100, null, null, 1266882676, 1131396187, 1149418875, 1257281062, 0, "SRX25308997", "SRS21984105", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.94345, 0.94707, 0.07428, 0.0741, 0.6898, 0.68856, 0.4653, 0.46918, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33175, "SRR29809747", "SRX25308996", "SRS21984104", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "pdx1 morpholino + 0mM STS 4", "GSM8393503", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS|geo loc name:missing|collection date:missing", "pdx1 morpholino + 0mM STS 4", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS", "GSM8393503", "GSM8393503: pdx1 morpholino + 0mM STS 4; Danio rerio; RNA Seq", "GSM8393503 r1", "GSM8393503", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "28_1.fq.gz 28_2.fq.gz", "fastq fastq", 4464066400.0, 22320332.0, "GSM8393503 r1", "0:100 1:100", "A:1209155509;C:1023407835;G:1040239673;T:1191263383;N:0", 100, 100, null, null, 1209155509, 1023407835, 1040239673, 1191263383, 0, "SRX25308996", "SRS21984104", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.934, 0.93723, 0.08814, 0.08601, 0.69834, 0.69798, 0.47533, 0.47611, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33176, "SRR29809748", "SRX25308995", "SRS21984103", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "pdx1 morpholino + 0mM STS 3", "GSM8393502", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS|geo loc name:missing|collection date:missing", "pdx1 morpholino + 0mM STS 3", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS", "GSM8393502", "GSM8393502: pdx1 morpholino + 0mM STS 3; Danio rerio; RNA Seq", "GSM8393502 r1", "GSM8393502", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "22_1.fq.gz 22_2.fq.gz", "fastq fastq", 4613819800.0, 23069099.0, "GSM8393502 r1", "0:100 1:100", "A:1218890904;C:1084874278;G:1104087523;T:1205967095;N:0", 100, 100, null, null, 1218890904, 1084874278, 1104087523, 1205967095, 0, "SRX25308995", "SRS21984103", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.9426, 0.94852, 0.07601, 0.07487, 0.69197, 0.69075, 0.45872, 0.45856, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33177, "SRR29809749", "SRX25308994", "SRS21984102", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "pdx1 morpholino + 0mM STS 2", "GSM8393501", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS|geo loc name:missing|collection date:missing", "pdx1 morpholino + 0mM STS 2", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS", "GSM8393501", "GSM8393501: pdx1 morpholino + 0mM STS 2; Danio rerio; RNA Seq", "GSM8393501 r1", "GSM8393501", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "16_1.fq.gz 16_2.fq.gz", "fastq fastq", 4818005000.0, 24090025.0, "GSM8393501 r1", "0:100 1:100", "A:1291680744;C:1114433015;G:1134463270;T:1277427971;N:0", 100, 100, null, null, 1291680744, 1114433015, 1134463270, 1277427971, 0, "SRX25308994", "SRS21984102", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.93988, 0.94257, 0.08614, 0.08554, 0.69376, 0.69367, 0.47178, 0.47111, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33178, "SRR29809750", "SRX25308993", "SRS21984101", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "pdx1 morpholino + 0mM STS 1", "GSM8393500", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS|geo loc name:missing|collection date:missing", "pdx1 morpholino + 0mM STS 1", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:pdx1|dose:0|agent:STS", "GSM8393500", "GSM8393500: pdx1 morpholino + 0mM STS 1; Danio rerio; RNA Seq", "GSM8393500 r1", "GSM8393500", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "10_2.fq.gz 10_1.fq.gz", "fastq fastq", 4827935800.0, 24139679.0, "GSM8393500 r1", "0:100 1:100", "A:1267823750;C:1143323623;G:1156194469;T:1260593958;N:0", 100, 100, null, null, 1267823750, 1143323623, 1156194469, 1260593958, 0, "SRX25308993", "SRS21984101", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.94483, 0.94829, 0.07178, 0.07025, 0.69077, 0.69025, 0.46181, 0.45982, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33179, "SRR29809751", "SRX25308992", "SRS21984100", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "Control morpholino + 20mM STS 5", "GSM8393499", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS|geo loc name:missing|collection date:missing", "Control morpholino + 20mM STS 5", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS", "GSM8393499", "GSM8393499: Control morpholino + 20mM STS 5; Danio rerio; RNA Seq", "GSM8393499 r1", "GSM8393499", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "9_1.fq.gz 9_2.fq.gz", "fastq fastq", 4822379000.0, 24111895.0, "GSM8393499 r1", "0:100 1:100", "A:1262977318;C:1145277730;G:1159167028;T:1254956924;N:0", 100, 100, null, null, 1262977318, 1145277730, 1159167028, 1254956924, 0, "SRX25308992", "SRS21984100", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.94642, 0.94964, 0.06863, 0.0674, 0.69288, 0.69252, 0.4574, 0.44372, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33180, "SRR29809752", "SRX25308991", "SRS21984099", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "Control morpholino + 20mM STS 4", "GSM8393498", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS|geo loc name:missing|collection date:missing", "Control morpholino + 20mM STS 4", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS", "GSM8393498", "GSM8393498: Control morpholino + 20mM STS 4; Danio rerio; RNA Seq", "GSM8393498 r1", "GSM8393498", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "3_1.fq.gz 3_2.fq.gz", "fastq fastq", 4803150200.0, 24015751.0, "GSM8393498 r1", "0:100 1:100", "A:1253239300;C:1144350399;G:1158671984;T:1246888517;N:0", 100, 100, null, null, 1253239300, 1144350399, 1158671984, 1246888517, 0, "SRX25308991", "SRS21984099", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.94606, 0.95015, 0.06543, 0.06441, 0.68676, 0.68611, 0.44857, 0.44396, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33181, "SRR29809753", "SRX25308990", "SRS21984098", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "Control morpholino + 20mM STS 3", "GSM8393497", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS|geo loc name:missing|collection date:missing", "Control morpholino + 20mM STS 3", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS", "GSM8393497", "GSM8393497: Control morpholino + 20mM STS 3; Danio rerio; RNA Seq", "GSM8393497 r1", "GSM8393497", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "27_1.fq.gz 27_2.fq.gz", "fastq fastq", 4277827200.0, 21389136.0, "GSM8393497 r1", "0:100 1:100", "A:1142589086;C:997230367;G:1005771965;T:1132235782;N:0", 100, 100, null, null, 1142589086, 997230367, 1005771965, 1132235782, 0, "SRX25308990", "SRS21984098", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.94201, 0.94596, 0.07754, 0.07484, 0.69794, 0.69617, 0.46286, 0.45985, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33182, "SRR29809754", "SRX25308989", "SRS21984097", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "Control morpholino + 20mM STS 2", "GSM8393496", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS|geo loc name:missing|collection date:missing", "Control morpholino + 20mM STS 2", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS", "GSM8393496", "GSM8393496: Control morpholino + 20mM STS 2; Danio rerio; RNA Seq", "GSM8393496 r1", "GSM8393496", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "21_2.fq.gz 21_1.fq.gz", "fastq fastq", 4019456600.0, 20097283.0, "GSM8393496 r1", "0:100 1:100", "A:1053249649;C:953992221;G:968100759;T:1044113971;N:0", 100, 100, null, null, 1053249649, 953992221, 968100759, 1044113971, 0, "SRX25308989", "SRS21984097", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.94377, 0.95125, 0.06861, 0.06745, 0.68676, 0.68523, 0.45049, 0.45168, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33183, "SRR29809755", "SRX25308988", "SRS21984096", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "Control morpholino + 20mM STS 1", "GSM8393495", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS|geo loc name:missing|collection date:missing", "Control morpholino + 20mM STS 1", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:20|agent:STS", "GSM8393495", "GSM8393495: Control morpholino + 20mM STS 1; Danio rerio; RNA Seq", "GSM8393495 r1", "GSM8393495", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "15_1.fq.gz 15_2.fq.gz", "fastq fastq", 4829679200.0, 24148396.0, "GSM8393495 r1", "0:100 1:100", "A:1292193191;C:1119414896;G:1140502241;T:1277568872;N:0", 100, 100, null, null, 1292193191, 1119414896, 1140502241, 1277568872, 0, "SRX25308988", "SRS21984096", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.9423, 0.9467, 0.07958, 0.07808, 0.69763, 0.69658, 0.46406, 0.46623, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33184, "SRR29809756", "SRX25308987", "SRS21984095", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "Control morpholino + 15mM STS 5", "GSM8393494", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS|geo loc name:missing|collection date:missing", "Control morpholino + 15mM STS 5", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS", "GSM8393494", "GSM8393494: Control morpholino + 15mM STS 5; Danio rerio; RNA Seq", "GSM8393494 r1", "GSM8393494", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "8_2.fq.gz 8_1.fq.gz", "fastq fastq", 4803709800.0, 24018549.0, "GSM8393494 r1", "0:100 1:100", "A:1253733589;C:1143748058;G:1158768340;T:1247459813;N:0", 100, 100, null, null, 1253733589, 1143748058, 1158768340, 1247459813, 0, "SRX25308987", "SRS21984095", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.94718, 0.94926, 0.06582, 0.06461, 0.68791, 0.68738, 0.44759, 0.44517, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33185, "SRR29809757", "SRX25308986", "SRS21984094", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "Control morpholino + 15mM STS 4", "GSM8393493", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS|geo loc name:missing|collection date:missing", "Control morpholino + 15mM STS 4", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS", "GSM8393493", "GSM8393493: Control morpholino + 15mM STS 4; Danio rerio; RNA Seq", "GSM8393493 r1", "GSM8393493", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "26_1.fq.gz 26_2.fq.gz", "fastq fastq", 4816718000.0, 24083590.0, "GSM8393493 r1", "0:100 1:100", "A:1278966223;C:1129131703;G:1144234415;T:1264385659;N:0", 100, 100, null, null, 1278966223, 1129131703, 1144234415, 1264385659, 0, "SRX25308986", "SRS21984094", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.94278, 0.94713, 0.07235, 0.0704, 0.69895, 0.698, 0.4536, 0.45416, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33186, "SRR29809758", "SRX25308985", "SRS21984093", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "Control morpholino + 15mM STS 3", "GSM8393492", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS|geo loc name:missing|collection date:missing", "Control morpholino + 15mM STS 3", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS", "GSM8393492", "GSM8393492: Control morpholino + 15mM STS 3; Danio rerio; RNA Seq", "GSM8393492 r1", "GSM8393492", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "20_2.fq.gz 20_1.fq.gz", "fastq fastq", 4825880400.0, 24129402.0, "GSM8393492 r1", "0:100 1:100", "A:1263053657;C:1147908238;G:1161094243;T:1253824262;N:0", 100, 100, null, null, 1263053657, 1147908238, 1161094243, 1253824262, 0, "SRX25308985", "SRS21984093", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.94642, 0.95164, 0.06472, 0.06312, 0.69035, 0.68909, 0.44854, 0.44216, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33187, "SRR29809759", "SRX25308984", "SRS21984092", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "Control morpholino + 15mM STS 2", "GSM8393491", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS|geo loc name:missing|collection date:missing", "Control morpholino + 15mM STS 2", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS", "GSM8393491", "GSM8393491: Control morpholino + 15mM STS 2; Danio rerio; RNA Seq", "GSM8393491 r1", "GSM8393491", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "2_1.fq.gz 2_2.fq.gz", "fastq fastq", 4805985200.0, 24029926.0, "GSM8393491 r1", "0:100 1:100", "A:1255841114;C:1143278337;G:1157783615;T:1249082134;N:0", 100, 100, null, null, 1255841114, 1143278337, 1157783615, 1249082134, 0, "SRX25308984", "SRS21984092", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.94666, 0.94794, 0.06553, 0.06456, 0.69181, 0.69175, 0.4359, 0.44559, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33188, "SRR29809760", "SRX25308983", "SRS21984091", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "Control morpholino + 15mM STS 1", "GSM8393490", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS|geo loc name:missing|collection date:missing", "Control morpholino + 15mM STS 1", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:15|agent:STS", "GSM8393490", "GSM8393490: Control morpholino + 15mM STS 1; Danio rerio; RNA Seq", "GSM8393490 r1", "GSM8393490", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "14_1.fq.gz 14_2.fq.gz", "fastq fastq", 4553465000.0, 22767325.0, "GSM8393490 r1", "0:100 1:100", "A:1209891078;C:1063666819;G:1082075995;T:1197831108;N:0", 100, 100, null, null, 1209891078, 1063666819, 1082075995, 1197831108, 0, "SRX25308983", "SRS21984091", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.9432, 0.94661, 0.07696, 0.07599, 0.69763, 0.69721, 0.46463, 0.46425, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33189, "SRR29809761", "SRX25308982", "SRS21984090", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "Control morpholino + 0mM STS 5", "GSM8393489", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS|geo loc name:missing|collection date:missing", "Control morpholino + 0mM STS 5", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS", "GSM8393489", "GSM8393489: Control morpholino + 0mM STS 5; Danio rerio; RNA Seq", "GSM8393489 r1", "GSM8393489", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "7_1.fq.gz 7_2.fq.gz", "fastq fastq", 4813770200.0, 24068851.0, "GSM8393489 r1", "0:100 1:100", "A:1251918123;C:1151936172;G:1164458418;T:1245457487;N:0", 100, 100, null, null, 1251918123, 1151936172, 1164458418, 1245457487, 0, "SRX25308982", "SRS21984090", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.95021, 0.95271, 0.06538, 0.06376, 0.69171, 0.68996, 0.44317, 0.4435, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33190, "SRR29809762", "SRX25308981", "SRS21984089", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "Control morpholino + 0mM STS 4", "GSM8393488", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS|geo loc name:missing|collection date:missing", "Control morpholino + 0mM STS 4", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS", "GSM8393488", "GSM8393488: Control morpholino + 0mM STS 4; Danio rerio; RNA Seq", "GSM8393488 r1", "GSM8393488", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "25_1.fq.gz 25_2.fq.gz", "fastq fastq", 4810346800.0, 24051734.0, "GSM8393488 r1", "0:100 1:100", "A:1275301780;C:1127999390;G:1144547869;T:1262497761;N:0", 100, 100, null, null, 1275301780, 1127999390, 1144547869, 1262497761, 0, "SRX25308981", "SRS21984089", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.94519, 0.94834, 0.06949, 0.06803, 0.69552, 0.69524, 0.44741, 0.45052, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33191, "SRR29809763", "SRX25308980", "SRS21984088", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "Control morpholino + 0mM STS 3", "GSM8393487", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS|geo loc name:missing|collection date:missing", "Control morpholino + 0mM STS 3", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS", "GSM8393487", "GSM8393487: Control morpholino + 0mM STS 3; Danio rerio; RNA Seq", "GSM8393487 r1", "GSM8393487", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "19_1.fq.gz 19_2.fq.gz", "fastq fastq", 4811704200.0, 24058521.0, "GSM8393487 r1", "0:100 1:100", "A:1257129134;C:1146835083;G:1160663520;T:1247076463;N:0", 100, 100, null, null, 1257129134, 1146835083, 1160663520, 1247076463, 0, "SRX25308980", "SRS21984088", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.94691, 0.95082, 0.06344, 0.06212, 0.69014, 0.69059, 0.45386, 0.43864, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33192, "SRR29809764", "SRX25308979", "SRS21984087", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "Control morpholino + 0mM STS 2", "GSM8393486", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS|geo loc name:missing|collection date:missing", "Control morpholino + 0mM STS 2", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS", "GSM8393486", "GSM8393486: Control morpholino + 0mM STS 2; Danio rerio; RNA Seq", "GSM8393486 r1", "GSM8393486", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "13_1.fq.gz 13_2.fq.gz", "fastq fastq", 4616178800.0, 23080894.0, "GSM8393486 r1", "0:100 1:100", "A:1225429879;C:1079094541;G:1096304865;T:1215349515;N:0", 100, 100, null, null, 1225429879, 1079094541, 1096304865, 1215349515, 0, "SRX25308979", "SRS21984087", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.94498, 0.9498, 0.07635, 0.075, 0.69319, 0.6927, 0.46598, 0.466, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [33193, "SRR29809765", "SRX25308978", "SRS21984086", "SRP519612", "PRJNA1135151", "The effect of sodium thiosulfate on hyperglycemic zebrafish larvae", "GSE272119", "Transcriptome Analysis", "We investigated the efficacy of sodium thiosulfate STS in treating hyperglycemia induced pronephros damage in zebrafish to gain insights into the underlying mechanisms. Our results demonstrate that STS treatment effectively restored pronephros damage induced by hyperglycemia. Hyperglycemia was induced in zebrafish by suppressing the pdx1 transcription factor  which plays a crucial role in maintaining physiological pancreatic function. The pronephros structure was analyzed at 48 hpf. Metabolomic profiling and RNA sequencing were conducted on groups subjected to various STS concentrations. Our findings reveal a downregulation of nitric oxide NO signaling in zebrafish with a knocked down pdx1 gene  both metabolomically and transcriptionally. Notably  treatment with STS led to a compensatory upregulation of NO signaling  as evidenced by preliminary metabolomic data  ultimately resulting in the rescue of the pronephros structure. Overall design: To analyze transcriptomic adaptations to STS  RNA seq of hyperglycemic zebrafish treated with 0 mM  15 mM  and 20 mM STS was conducted. Zebrafish from a control group exposed to the same STS concentrations were analyzed simultaneously. Hyperglycemia in zebrafish was induced via morpholino technology targeting the transcription factor pdx1  which is responsible for physiological pancreatic development. A control morpholino was injected into zebrafish of the control group. RNA was isolated at 48 hpf. The transgenic zebrafish line Tgwt1b:EGFP was used for experimental procedure. Next to RNA seq analysis  a metabolomic profiling of similar experimental groups was performed.", null, "pubmed:39264236", null, "Control morpholino + 0mM STS 1", "GSM8393485", null, "source name:larvae|tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS|geo loc name:missing|collection date:missing", "Control morpholino + 0mM STS 1", "trimmed with trim galore version 0.6.4. Parameters:   length 26   phred33 Get raw counts with kallisto quant version 0.4.6. CPM estimates  generated with cpm function from edgeR version 3.17 Assembly: GRCz11 Supplementary files format and content: raw counts with kallisto quant version 0.4.6. Supplementary files format and content: CPM estimates  generated with cpm function from edgeR version 3.17", "larvae", null, "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "tissue:larvae|strain:Tgwt1b:EGFP|genotype:ctrl|dose:0|agent:STS", "GSM8393485", "GSM8393485: Control morpholino + 0mM STS 1; Danio rerio; RNA Seq", "GSM8393485 r1", "GSM8393485", "1", "RNA was isolated from whole body samples from zebrafish larvae at 48hpf using the RNeasy Mini Kit from QIAGEN Hilden  173 Germany. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "BGISEQ-500", null, "SRP519612", null, null, "1_1.fq.gz 1_2.fq.gz", "fastq fastq", 4823953400.0, 24119767.0, "GSM8393485 r1", "0:100 1:100", "A:1270954678;C:1137736456;G:1155516940;T:1259745326;N:0", 100, 100, null, null, 1270954678, 1137736456, 1155516940, 1259745326, 0, "SRX25308978", "SRS21984086", "SRA1923353", "ZMF, University Heidelberg", "ZMF, University Heidelberg", 2, 0.94325, 0.94699, 0.06928, 0.06864, 0.69372, 0.69307, 0.44844, 0.45647, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "Germany", "2024-07-12", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34206, "SRR31539731", "SRX26906755", "SRS23386341", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 7 dpf sox10 mutant embryos   biol rep 3", "GSM8655460", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:7 dpf|geo loc name:missing|collection date:missing", "Whole body 7 dpf sox10 mutant embryos   biol rep 3", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:7 dpf", "GSM8655460", "GSM8655460: Whole body 7 dpf sox10 mutant embryos   biol rep 3; Danio rerio; RNA Seq", "GSM8655460 r1", "GSM8655460", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "7 dpf_mut 3_R1.fastq.gz 7 dpf_mut 3_R2.fastq.gz", "fastq fastq", 14265929756.0, 47238178.0, "GSM8655460 r1", "0:151 1:151", "A:3890017873;C:3282588566;G:3079614796;T:4012518928;N:1189593", 151, 151, null, null, 3890017873, 3282588566, 3079614796, 4012518928, 1189593, "SRX26906755", "SRS23386341", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34207, "SRR31539732", "SRX26906754", "SRS23386340", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 7 dpf sox10 mutant embryos   biol rep 2", "GSM8655459", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:7 dpf|geo loc name:missing|collection date:missing", "Whole body 7 dpf sox10 mutant embryos   biol rep 2", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:7 dpf", "GSM8655459", "GSM8655459: Whole body 7 dpf sox10 mutant embryos   biol rep 2; Danio rerio; RNA Seq", "GSM8655459 r1", "GSM8655459", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "7 dpf_mut 2_R1.fastq.gz 7 dpf_mut 2_R2.fastq.gz", "fastq fastq", 16096968138.0, 53301219.0, "GSM8655459 r1", "0:151 1:151", "A:4158085994;C:3672102993;G:3915623401;T:4349806816;N:1348934", 151, 151, null, null, 4158085994, 3672102993, 3915623401, 4349806816, 1348934, "SRX26906754", "SRS23386340", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34208, "SRR31539733", "SRX26906753", "SRS23386339", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 7 dpf sox10 mutant embryos   biol rep 1", "GSM8655458", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:7 dpf|geo loc name:missing|collection date:missing", "Whole body 7 dpf sox10 mutant embryos   biol rep 1", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:7 dpf", "GSM8655458", "GSM8655458: Whole body 7 dpf sox10 mutant embryos   biol rep 1; Danio rerio; RNA Seq", "GSM8655458 r1", "GSM8655458", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "7 dpf_mut 1_R1.fastq.gz 7 dpf_mut 1_R2.fastq.gz", "fastq fastq", 15919165034.0, 52712467.0, "GSM8655458 r1", "0:151 1:151", "A:4153549187;C:3626188288;G:3782139805;T:4355972996;N:1314758", 151, 151, null, null, 4153549187, 3626188288, 3782139805, 4355972996, 1314758, "SRX26906753", "SRS23386339", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34209, "SRR31539734", "SRX26906752", "SRS23386338", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 7 dpf wild type embryos   biol rep 3", "GSM8655457", null, "source name:whole body|tissue:whole body|genotype:WT|time:7 dpf|geo loc name:missing|collection date:missing", "Whole body 7 dpf wild type embryos   biol rep 3", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:7 dpf", "GSM8655457", "GSM8655457: Whole body 7 dpf wild type embryos   biol rep 3; Danio rerio; RNA Seq", "GSM8655457 r1", "GSM8655457", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "7 dpf_WT 3_R1.fastq.gz 7 dpf_WT 3_R2.fastq.gz", "fastq fastq", 15543953590.0, 51470045.0, "GSM8655457 r1", "0:151 1:151", "A:4031818994;C:3704599213;G:3577251498;T:4228986622;N:1297263", 151, 151, null, null, 4031818994, 3704599213, 3577251498, 4228986622, 1297263, "SRX26906752", "SRS23386338", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34210, "SRR31539735", "SRX26906751", "SRS23386337", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 7 dpf wild type embryos   biol rep 2", "GSM8655456", null, "source name:whole body|tissue:whole body|genotype:WT|time:7 dpf|geo loc name:missing|collection date:missing", "Whole body 7 dpf wild type embryos   biol rep 2", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:7 dpf", "GSM8655456", "GSM8655456: Whole body 7 dpf wild type embryos   biol rep 2; Danio rerio; RNA Seq", "GSM8655456 r1", "GSM8655456", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "7 dpf_WT 2_R1.fastq.gz 7 dpf_WT 2_R2.fastq.gz", "fastq fastq", 14325089744.0, 47434072.0, "GSM8655456 r1", "0:151 1:151", "A:3806636861;C:3343198938;G:3185927363;T:3988104951;N:1221631", 151, 151, null, null, 3806636861, 3343198938, 3185927363, 3988104951, 1221631, "SRX26906751", "SRS23386337", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34211, "SRR31539736", "SRX26906750", "SRS23386333", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 7 dpf wild type embryos   biol rep 1", "GSM8655455", null, "source name:whole body|tissue:whole body|genotype:WT|time:7 dpf|geo loc name:missing|collection date:missing", "Whole body 7 dpf wild type embryos   biol rep 1", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:7 dpf", "GSM8655455", "GSM8655455: Whole body 7 dpf wild type embryos   biol rep 1; Danio rerio; RNA Seq", "GSM8655455 r1", "GSM8655455", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "7 dpf_WT 1_R1.fastq.gz 7 dpf_WT 1_R2.fastq.gz", "fastq fastq", 16398118008.0, 54298404.0, "GSM8655455 r1", "0:151 1:151", "A:4341778579;C:3858758690;G:3657590940;T:4538608543;N:1381256", 151, 151, null, null, 4341778579, 3858758690, 3657590940, 4538608543, 1381256, "SRX26906750", "SRS23386333", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34212, "SRR31539737", "SRX26906749", "SRS23386334", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 4 dpf sox10 mutant embryos   biol rep 3", "GSM8655454", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:4 dpf|geo loc name:missing|collection date:missing", "Whole body 4 dpf sox10 mutant embryos    biol rep 3", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:4 dpf", "GSM8655454", "GSM8655454: Whole body 4 dpf sox10 mutant embryos    biol rep 3; Danio rerio; RNA Seq", "GSM8655454 r1", "GSM8655454", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "4 dpf_mut 3_R1.fastq.gz 4 dpf_mut 3_R2.fastq.gz", "fastq fastq", 15071278894.0, 49904897.0, "GSM8655454 r1", "0:151 1:151", "A:3996223512;C:3537174277;G:3398338576;T:4138304072;N:1238457", 151, 151, null, null, 3996223512, 3537174277, 3398338576, 4138304072, 1238457, "SRX26906749", "SRS23386334", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34213, "SRR31539738", "SRX26906748", "SRS23386336", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 4 dpf sox10 mutant embryos   biol rep 2", "GSM8655453", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:4 dpf|geo loc name:missing|collection date:missing", "Whole body 4 dpf sox10 mutant embryos    biol rep 2", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:4 dpf", "GSM8655453", "GSM8655453: Whole body 4 dpf sox10 mutant embryos    biol rep 2; Danio rerio; RNA Seq", "GSM8655453 r1", "GSM8655453", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "4 dpf_mut 2_R1.fastq.gz 4 dpf_mut 2_R2.fastq.gz", "fastq fastq", 14918687958.0, 49399629.0, "GSM8655453 r1", "0:151 1:151", "A:3994132161;C:3464356999;G:3293001897;T:4165943265;N:1253636", 151, 151, null, null, 3994132161, 3464356999, 3293001897, 4165943265, 1253636, "SRX26906748", "SRS23386336", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34214, "SRR31539739", "SRX26906747", "SRS23386332", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 4 dpf sox10 mutant embryos   biol rep 1", "GSM8655452", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:4 dpf|geo loc name:missing|collection date:missing", "Whole body 4 dpf sox10 mutant embryos    biol rep 1", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:4 dpf", "GSM8655452", "GSM8655452: Whole body 4 dpf sox10 mutant embryos    biol rep 1; Danio rerio; RNA Seq", "GSM8655452 r1", "GSM8655452", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "4 dpf_mut 1_R1.fastq.gz 4 dpf_mut 1_R2.fastq.gz", "fastq fastq", 14573247372.0, 48255786.0, "GSM8655452 r1", "0:151 1:151", "A:3964700989;C:3340575136;G:3128233836;T:4138502375;N:1235036", 151, 151, null, null, 3964700989, 3340575136, 3128233836, 4138502375, 1235036, "SRX26906747", "SRS23386332", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34215, "SRR31539740", "SRX26906746", "SRS23386331", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 4 dpf wild type embryos   biol rep 3", "GSM8655451", null, "source name:whole body|tissue:whole body|genotype:WT|time:4 dpf|geo loc name:missing|collection date:missing", "Whole body 4 dpf wild type embryos   biol rep 3", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:4 dpf", "GSM8655451", "GSM8655451: Whole body 4 dpf wild type embryos   biol rep 3; Danio rerio; RNA Seq", "GSM8655451 r1", "GSM8655451", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "4 dpf_WT 3_R1.fastq.gz 4 dpf_WT 3_R2.fastq.gz", "fastq fastq", 15132219172.0, 50106686.0, "GSM8655451 r1", "0:151 1:151", "A:4030654907;C:3519071260;G:3404455031;T:4176756699;N:1281275", 151, 151, null, null, 4030654907, 3519071260, 3404455031, 4176756699, 1281275, "SRX26906746", "SRS23386331", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34216, "SRR31539741", "SRX26906745", "SRS23386335", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 4 dpf wild type embryos   biol rep 2", "GSM8655450", null, "source name:whole body|tissue:whole body|genotype:WT|time:4 dpf|geo loc name:missing|collection date:missing", "Whole body 4 dpf wild type embryos   biol rep 2", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:4 dpf", "GSM8655450", "GSM8655450: Whole body 4 dpf wild type embryos   biol rep 2; Danio rerio; RNA Seq", "GSM8655450 r1", "GSM8655450", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "4 dpf_WT 2_R1.fastq.gz 4 dpf_WT 2_R2.fastq.gz", "fastq fastq", 15546478914.0, 51478407.0, "GSM8655450 r1", "0:151 1:151", "A:4105803894;C:3606318412;G:3589944905;T:4243130619;N:1281084", 151, 151, null, null, 4105803894, 3606318412, 3589944905, 4243130619, 1281084, "SRX26906745", "SRS23386335", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34217, "SRR31539742", "SRX26906744", "SRS23386330", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 4 dpf wild type embryos   biol rep 1", "GSM8655449", null, "source name:whole body|tissue:whole body|genotype:WT|time:4 dpf|geo loc name:missing|collection date:missing", "Whole body 4 dpf wild type embryos   biol rep 1", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:4 dpf", "GSM8655449", "GSM8655449: Whole body 4 dpf wild type embryos   biol rep 1; Danio rerio; RNA Seq", "GSM8655449 r1", "GSM8655449", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "4 dpf_WT 1_R1.fastq.gz 4 dpf_WT 1_R2.fastq.gz", "fastq fastq", 15246602880.0, 50485440.0, "GSM8655449 r1", "0:151 1:151", "A:4017771448;C:3536729749;G:3495956173;T:4194910365;N:1235145", 151, 151, null, null, 4017771448, 3536729749, 3495956173, 4194910365, 1235145, "SRX26906744", "SRS23386330", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34218, "SRR31539743", "SRX26906743", "SRS23386329", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 45 hpf sox10 mutant embryos   biol rep 3", "GSM8655448", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:45 hpf|geo loc name:missing|collection date:missing", "Whole body 45 hpf sox10 mutant embryos   biol rep 3", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:45 hpf", "GSM8655448", "GSM8655448: Whole body 45 hpf sox10 mutant embryos   biol rep 3; Danio rerio; RNA Seq", "GSM8655448 r1", "GSM8655448", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "45 hpf_mut 3_R1.fastq.gz 45 hpf_mut 3_R2.fastq.gz", "fastq fastq", 14338321572.0, 47477886.0, "GSM8655448 r1", "0:151 1:151", "A:3808719246;C:3382555065;G:3212075099;T:3933758367;N:1213795", 151, 151, null, null, 3808719246, 3382555065, 3212075099, 3933758367, 1213795, "SRX26906743", "SRS23386329", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34219, "SRR31539744", "SRX26906742", "SRS23386326", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 45 hpf sox10 mutant embryos   biol rep 2", "GSM8655447", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:45 hpf|geo loc name:missing|collection date:missing", "Whole body 45 hpf sox10 mutant embryos   biol rep 2", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:45 hpf", "GSM8655447", "GSM8655447: Whole body 45 hpf sox10 mutant embryos   biol rep 2; Danio rerio; RNA Seq", "GSM8655447 r1", "GSM8655447", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "45 hpf_mut 2_R1.fastq.gz 45 hpf_mut 2_R2.fastq.gz", "fastq fastq", 15462167158.0, 51199229.0, "GSM8655447 r1", "0:151 1:151", "A:4089691508;C:3622289242;G:3495097207;T:4253826187;N:1263014", 151, 151, null, null, 4089691508, 3622289242, 3495097207, 4253826187, 1263014, "SRX26906742", "SRS23386326", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34220, "SRR31539745", "SRX26906741", "SRS23386327", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 45 hpf sox10 mutant embryos   biol rep 1", "GSM8655446", null, "source name:whole body|tissue:whole body|genotype:sox10 / |time:45 hpf|geo loc name:missing|collection date:missing", "Whole body 45 hpf sox10 mutant embryos   biol rep 1", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:sox10 / |time:45 hpf", "GSM8655446", "GSM8655446: Whole body 45 hpf sox10 mutant embryos   biol rep 1; Danio rerio; RNA Seq", "GSM8655446 r1", "GSM8655446", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "45 hpf_mut 1_R1.fastq.gz 45 hpf_mut 1_R2.fastq.gz", "fastq fastq", 15655817712.0, 51840456.0, "GSM8655446 r1", "0:151 1:151", "A:4157360171;C:3674570903;G:3484564544;T:4338002005;N:1320089", 151, 151, null, null, 4157360171, 3674570903, 3484564544, 4338002005, 1320089, "SRX26906741", "SRS23386327", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34221, "SRR31539746", "SRX26906740", "SRS23386328", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 45 hpf wild type embryos   biol rep 3", "GSM8655445", null, "source name:whole body|tissue:whole body|genotype:WT|time:45 hpf|geo loc name:missing|collection date:missing", "Whole body 45 hpf wild type embryos   biol rep 3", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:45 hpf", "GSM8655445", "GSM8655445: Whole body 45 hpf wild type embryos   biol rep 3; Danio rerio; RNA Seq", "GSM8655445 r1", "GSM8655445", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "45 hpf_WT 3_R1.fastq.gz 45 hpf_WT 3_R2.fastq.gz", "fastq fastq", 14580346184.0, 48279292.0, "GSM8655445 r1", "0:151 1:151", "A:3858927638;C:3450290173;G:3271701209;T:3998202503;N:1224661", 151, 151, null, null, 3858927638, 3450290173, 3271701209, 3998202503, 1224661, "SRX26906740", "SRS23386328", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34222, "SRR31539747", "SRX26906739", "SRS23386325", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 45 hpf wild type embryos   biol rep 2", "GSM8655444", null, "source name:whole body|tissue:whole body|genotype:WT|time:45 hpf|geo loc name:missing|collection date:missing", "Whole body 45 hpf wild type embryos   biol rep 2", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:45 hpf", "GSM8655444", "GSM8655444: Whole body 45 hpf wild type embryos   biol rep 2; Danio rerio; RNA Seq", "GSM8655444 r1", "GSM8655444", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "45 hpf_WT 2_R1.fastq.gz 45 hpf_WT_2_R2.fastq.gz", "fastq fastq", 15005198878.0, 49686089.0, "GSM8655444 r1", "0:151 1:151", "A:3950487195;C:3509517845;G:3418800225;T:4125159820;N:1233793", 151, 151, null, null, 3950487195, 3509517845, 3418800225, 4125159820, 1233793, "SRX26906739", "SRS23386325", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [34223, "SRR31539748", "SRX26906738", "SRS23386324", "SRP548139", "PRJNA1191617", "Sox10 is required for systemic initiation of bone mineralization", "GSE283071", "Transcriptome Analysis", "Heterozygous variants in SOX10 cause syndromes affecting pigmentation  digestion  hearing  and neural development  primarily attributable to failed differentiation or loss of non skeletal neural crest derivatives. We report here an additional novel requirement for Sox10 in bone mineralization. Neither crest  nor mesoderm derived bones initiate mineralization on time in zebrafish sox10 mutants  despite normal osteoblast differentiation and matrix production. Mutants are deficient in the Trpv6+ ionocytes that take up calcium from the environment  resulting in severe calcium deficiency. As these ionocytes derive from ectoderm  not crest  we hypothesized that the primary defect resides in a separate organ that systemically regulates ionocyte numbers. RNAseq revealed significantly elevated stanniocalcin Stc1a  an anti hypercalcemic hormone  in sox10 mutants. Stc1a inhibits calcium uptake in fish by repressing trpv6 expression and Trpv6+ ionocyte proliferation. Epistasis assays confirm excess Stc1a as the proximate cause of the calcium deficit. The pronephros derived glands that synthesize Stc1a interact with sox10+ cells  but these cells are missing in mutants. We conclude that sox10+ crest derived cells non autonomously limit Stc1a production to allow the inaugural wave of calcium uptake necessary to initiate bone mineralization. Overall design: Bulk RNA seq was performed on pooled whole body zebrafish wild type and sox10 mutant larvae at 45 hpf  4 dpf and 7 dpf.  Total of 18 samples. 45 hpf 3 replicates: controls n = 10  20 & 25; mutants n = 10 15 & 15 embryos  4 dpf 3 replicates: controls n = 10  15 & 12; mutants n = 10 11 & 12 embryos and 7 dpf 3 replicates: controls n = 12  30 & 18; mutants = 18  12 & 7 embryos", null, "pubmed:39791977", null, "Whole body 45 hpf wild type embryos   biol rep 1", "GSM8655443", null, "source name:whole body|tissue:whole body|genotype:WT|time:45 hpf|geo loc name:missing|collection date:missing", "Whole body 45 hpf wild type embryos   biol rep 1", "The data was processed through the Galaxy project using Trimmomatic version 0.39 Sequences were pseudoaligned and quantified at TPM values using Kallisto. Assembly: GRCz11 Supplementary files format and content: Tab delimited text file includes TPM values for each transcript at 45 hpf  4 dpf and 7 dpf", "whole body", null, "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina\u2019s TruSeq\u00ae stranded mRNA library preparation kit.", null, "tissue:whole body|genotype:WT|time:45 hpf", "GSM8655443", "GSM8655443: Whole body 45 hpf wild type embryos   biol rep 1; Danio rerio; RNA Seq", "GSM8655443 r1", "GSM8655443", "1", "RNA was extracted using the RNAqueous 4PCR Total RNA Isolation Kit Invitrogen 150 to 300 ng of total RNA determined by InvitrogenTM QubitTM high sensitivity spectrofluorometric measurement was poly A selected and reverse transcribed using Illumina's TruSeq\u00ae stranded mRNA library preparation kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP548139", null, null, "45 hpf_WT 1_R1.fastq.gz 45 hpf_WT 1_R2.fastq.gz", "fastq fastq", 14884992912.0, 49288056.0, "GSM8655443 r1", "0:151 1:151", "A:3878762924;C:3475070121;G:3485186845;T:4044768200;N:1204822", 151, 151, null, null, 3878762924, 3475070121, 3485186845, 4044768200, 1204822, "SRX26906738", "SRS23386324", null, null, "Barske Lab, Human Genetics, Cincinnati Children's Hospital", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "trueseq", "bulk", "bulk", "bulk", null, "United States", "2024-11-27", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [36227, "SRR33613672", "SRX28842027", "SRS25072222", "SRP586119", "PRJNA1263917", "Danio rerio Transcriptome or Gene expression", "PRJNA1263917", "Other", "Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.", null, null, null, "Danio rerio", "Danio rerio", null, "strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:7 day|dev stage:Juvenile fish|collection date:2024 04 16|geo loc name:China: Hang Zhou|sex:missing|tissue:Whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "HFD 3", "HFD 3", "Total RNA was extracted  digested with DNase I  and mRNA enriched. post fragmentation  cDNA synthesis  and library construction  the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP586119", null, null, "HFD-3-1.fq.gz HFD-3-2.fq.gz", "fastq fastq", 6810755100.0, 22702517.0, "HFD 3 1.fq.gz", "0:150 1:150", "A:1804127778;C:1596175018;G:1609090701;T:1801361603;N:0", 150, 150, null, null, 1804127778, 1596175018, 1609090701, 1801361603, 0, "SRX28842027", "SRS25072222", "SRA2131918", "Yibin University|Faculty of Quality Management and Inspection &amp; Qua", "Yibin University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-05-18", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [36228, "SRR33613673", "SRX28842026", "SRS25072222", "SRP586119", "PRJNA1263917", "Danio rerio Transcriptome or Gene expression", "PRJNA1263917", "Other", "Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.", null, null, null, "Danio rerio", "Danio rerio", null, "strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:7 day|dev stage:Juvenile fish|collection date:2024 04 16|geo loc name:China: Hang Zhou|sex:missing|tissue:Whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "HFD 2", "HFD 2", "Total RNA was extracted  digested with DNase I  and mRNA enriched. post fragmentation  cDNA synthesis  and library construction  the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP586119", null, null, "HFD-2-1.fq.gz HFD-2-2.fq.gz", "fastq fastq", 6826358400.0, 22754528.0, "HFD 2 1.fq.gz", "0:150 1:150", "A:1826465185;C:1582322712;G:1596188986;T:1821381517;N:0", 150, 150, null, null, 1826465185, 1582322712, 1596188986, 1821381517, 0, "SRX28842026", "SRS25072222", "SRA2131918", "Yibin University|Faculty of Quality Management and Inspection &amp; Qua", "Yibin University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-05-18", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [36229, "SRR33613674", "SRX28842025", "SRS25072222", "SRP586119", "PRJNA1263917", "Danio rerio Transcriptome or Gene expression", "PRJNA1263917", "Other", "Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.", null, null, null, "Danio rerio", "Danio rerio", null, "strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:7 day|dev stage:Juvenile fish|collection date:2024 04 16|geo loc name:China: Hang Zhou|sex:missing|tissue:Whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "HFD 1", "HFD 1", "Total RNA was extracted  digested with DNase I  and mRNA enriched. post fragmentation  cDNA synthesis  and library construction  the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP586119", null, null, "HFD-1-1.fq.gz HFD-1-2.fq.gz", "fastq fastq", 6598410300.0, 21994701.0, "HFD 1 1.fq.gz", "0:150 1:150", "A:1765905584;C:1529581410;G:1542056821;T:1760866485;N:0", 150, 150, null, null, 1765905584, 1529581410, 1542056821, 1760866485, 0, "SRX28842025", "SRS25072222", "SRA2131918", "Yibin University|Faculty of Quality Management and Inspection &amp; Qua", "Yibin University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-05-18", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [36230, "SRR33613675", "SRX28842024", "SRS25072222", "SRP586119", "PRJNA1263917", "Danio rerio Transcriptome or Gene expression", "PRJNA1263917", "Other", "Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.", null, null, null, "Danio rerio", "Danio rerio", null, "strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:7 day|dev stage:Juvenile fish|collection date:2024 04 16|geo loc name:China: Hang Zhou|sex:missing|tissue:Whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "HFD10 3", "HFD10 3", "Total RNA was extracted  digested with DNase I  and mRNA enriched. post fragmentation  cDNA synthesis  and library construction  the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP586119", null, null, "HFD10-3-1.fq.gz HFD10-3-2.fq.gz", "fastq fastq", 6609153300.0, 22030511.0, "HFD10 3 1.fq.gz", "0:150 1:150", "A:1780787716;C:1521027085;G:1532800826;T:1774537673;N:0", 150, 150, null, null, 1780787716, 1521027085, 1532800826, 1774537673, 0, "SRX28842024", "SRS25072222", "SRA2131918", "Yibin University|Faculty of Quality Management and Inspection &amp; Qua", "Yibin University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-05-18", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [36231, "SRR33613676", "SRX28842023", "SRS25072222", "SRP586119", "PRJNA1263917", "Danio rerio Transcriptome or Gene expression", "PRJNA1263917", "Other", "Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.", null, null, null, "Danio rerio", "Danio rerio", null, "strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:7 day|dev stage:Juvenile fish|collection date:2024 04 16|geo loc name:China: Hang Zhou|sex:missing|tissue:Whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "HFD10 2", "HFD10 2", "Total RNA was extracted  digested with DNase I  and mRNA enriched. post fragmentation  cDNA synthesis  and library construction  the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP586119", null, null, "HFD10-2-1.fq.gz HFD10-2-2.fq.gz", "fastq fastq", 6605145900.0, 22017153.0, "HFD10 2 1.fq.gz", "0:150 1:150", "A:1765731508;C:1533254667;G:1545960098;T:1760199627;N:0", 150, 150, null, null, 1765731508, 1533254667, 1545960098, 1760199627, 0, "SRX28842023", "SRS25072222", "SRA2131918", "Yibin University|Faculty of Quality Management and Inspection &amp; Qua", "Yibin University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-05-18", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [36232, "SRR33613677", "SRX28842022", "SRS25072222", "SRP586119", "PRJNA1263917", "Danio rerio Transcriptome or Gene expression", "PRJNA1263917", "Other", "Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.", null, null, null, "Danio rerio", "Danio rerio", null, "strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:7 day|dev stage:Juvenile fish|collection date:2024 04 16|geo loc name:China: Hang Zhou|sex:missing|tissue:Whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "HFD10 1", "HFD10 1", "Total RNA was extracted  digested with DNase I  and mRNA enriched. post fragmentation  cDNA synthesis  and library construction  the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP586119", null, null, "HFD10-1-1.fq.gz HFD10-1-2.fq.gz", "fastq fastq", 6780056700.0, 22600189.0, "HFD10 1 1.fq.gz", "0:150 1:150", "A:1819443100;C:1566081115;G:1580525465;T:1814007020;N:0", 150, 150, null, null, 1819443100, 1566081115, 1580525465, 1814007020, 0, "SRX28842022", "SRS25072222", "SRA2131918", "Yibin University|Faculty of Quality Management and Inspection &amp; Qua", "Yibin University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-05-18", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [36233, "SRR33613678", "SRX28842021", "SRS25072222", "SRP586119", "PRJNA1263917", "Danio rerio Transcriptome or Gene expression", "PRJNA1263917", "Other", "Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.", null, null, null, "Danio rerio", "Danio rerio", null, "strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:7 day|dev stage:Juvenile fish|collection date:2024 04 16|geo loc name:China: Hang Zhou|sex:missing|tissue:Whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "NFD 3", "NFD 3", "Total RNA was extracted  digested with DNase I  and mRNA enriched. post fragmentation  cDNA synthesis  and library construction  the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP586119", null, null, "NFD-3-1.fq.gz NFD-3-2.fq.gz", "fastq fastq", 6677775900.0, 22259253.0, "NFD 3 1.fq.gz", "0:150 1:150", "A:1794821611;C:1541478212;G:1552820105;T:1788655972;N:0", 150, 150, null, null, 1794821611, 1541478212, 1552820105, 1788655972, 0, "SRX28842021", "SRS25072222", "SRA2131918", "Yibin University|Faculty of Quality Management and Inspection &amp; Qua", "Yibin University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-05-18", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [36234, "SRR33613679", "SRX28842020", "SRS25072222", "SRP586119", "PRJNA1263917", "Danio rerio Transcriptome or Gene expression", "PRJNA1263917", "Other", "Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.", null, null, null, "Danio rerio", "Danio rerio", null, "strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:7 day|dev stage:Juvenile fish|collection date:2024 04 16|geo loc name:China: Hang Zhou|sex:missing|tissue:Whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "NFD 2", "NFD 2", "Total RNA was extracted  digested with DNase I  and mRNA enriched. post fragmentation  cDNA synthesis  and library construction  the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP586119", null, null, "NFD-2-1.fq.gz NFD-2-2.fq.gz", "fastq fastq", 6680197200.0, 22267324.0, "NFD 2 1.fq.gz", "0:150 1:150", "A:1810744167;C:1526383805;G:1539949310;T:1803119918;N:0", 150, 150, null, null, 1810744167, 1526383805, 1539949310, 1803119918, 0, "SRX28842020", "SRS25072222", "SRA2131918", "Yibin University|Faculty of Quality Management and Inspection &amp; Qua", "Yibin University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-05-18", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [36235, "SRR33613680", "SRX28842019", "SRS25072222", "SRP586119", "PRJNA1263917", "Danio rerio Transcriptome or Gene expression", "PRJNA1263917", "Other", "Analyze the effect of TB KW fermentation on gene expression in high lipid zebrafish.", null, null, null, "Danio rerio", "Danio rerio", null, "strain:missing|isolate:missing|breed:missing|cultivar:missing|ecotype:missing|age:7 day|dev stage:Juvenile fish|collection date:2024 04 16|geo loc name:China: Hang Zhou|sex:missing|tissue:Whole body|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of Danio rerio", "NFD 1", "NFD 1", "Total RNA was extracted  digested with DNase I  and mRNA enriched. post fragmentation  cDNA synthesis  and library construction  the final single stranded DNA nanoball library was generated for sequencing via rolling circle replication.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "PolyA", "PAIRED", "DNBSEQ", "DNBSEQ-T7", null, "SRP586119", null, null, "NFD-1-1.fq.gz NFD-1-2.fq.gz", "fastq fastq", 6587923800.0, 21959746.0, "NFD 1 1.fq.gz", "0:150 1:150", "A:1773646514;C:1516320091;G:1530275621;T:1767681574;N:0", 150, 150, null, null, 1773646514, 1516320091, 1530275621, 1767681574, 0, "SRX28842019", "SRS25072222", "SRA2131918", "Yibin University|Faculty of Quality Management and Inspection &amp; Qua", "Yibin University", null, null, null, null, null, null, null, null, null, null, null, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2025-05-18", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [42197, "SRR5485641", "SRX2768777", "SRS2152486", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "A 3.0.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.0.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "A 3.0.2", "A 3.0.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_4.A_R1.fastq.gz HI.4096.008.Index_4.A_R1.fastq.gz", "fastq fastq", 2072387100.0, 20723871.0, "HI.4079.001.Index 4.A R1.fastq.gz", "0:100 1:0", "A:539231555;C:478779687;G:466992364;T:587014266;N:369228", 100, 0, null, null, 539231555, 478779687, 466992364, 587014266, 369228, "SRX2768777", "SRS2152486", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.94094, null, 0.13282, null, 0.67566, null, 0.46135, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42198, "SRR5485640", "SRX2768776", "SRS2152485", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "B 3.5.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.5.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "B 3.5.2", "B 3.5.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_5.B_R1.fastq.gz HI.4096.008.Index_5.B_R1.fastq.gz", "fastq fastq", 2236492200.0, 22364922.0, "HI.4079.001.Index 5.B R1.fastq.gz", "0:100 1:0", "A:580646206;C:518191209;G:502712894;T:634542622;N:399269", 100, 0, null, null, 580646206, 518191209, 502712894, 634542622, 399269, "SRX2768776", "SRS2152485", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.94188, null, 0.13073, null, 0.67653, null, 0.4635, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42199, "SRR5485639", "SRX2768775", "SRS2152484", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "C 3.20.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.20.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "C 3.20.2", "C 3.20.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_12.C_R1.fastq.gz HI.4096.008.Index_12.C_R1.fastq.gz", "fastq fastq", 1979628000.0, 19796280.0, "HI.4079.001.Index 12.C R1.fastq.gz", "0:100 1:0", "A:519406228;C:453563284;G:442115002;T:564195493;N:347993", 100, 0, null, null, 519406228, 453563284, 442115002, 564195493, 347993, "SRX2768775", "SRS2152484", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93946, null, 0.14364, null, 0.6759, null, 0.46247, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42200, "SRR5485638", "SRX2768774", "SRS2152483", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "D 3.0.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.0.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "D 3.0.14", "D 3.0.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_19.D_R1.fastq.gz HI.4096.008.Index_19.D_R1.fastq.gz", "fastq fastq", 1856095600.0, 18560956.0, "HI.4079.001.Index 19.D R1.fastq.gz", "0:100 1:0", "A:492424946;C:416504198;G:409645413;T:537196088;N:324955", 100, 0, null, null, 492424946, 416504198, 409645413, 537196088, 324955, "SRX2768774", "SRS2152483", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.9288, null, 0.15497, null, 0.69232, null, 0.46842, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42201, "SRR5485637", "SRX2768773", "SRS2152481", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "E 3.5.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.5.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "E 3.5.14", "E 3.5.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4096.008.Index_1.E_R1.fastq.gz HI.4079.001.Index_1.E_R1.fastq.gz", "fastq fastq", 2936761500.0, 29367615.0, "HI.4079.001.Index 1.E R1.fastq.gz", "0:100 1:0", "A:762661816;C:675701333;G:661832769;T:836033713;N:531869", 100, 0, null, null, 762661816, 675701333, 661832769, 836033713, 531869, "SRX2768773", "SRS2152481", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93957, null, 0.12499, null, 0.67714, null, 0.4697, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2017-05-08", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42202, "SRR5485636", "SRX2768772", "SRS2152480", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "F 3.20.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:3.20.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "F 3.20.14", "F 3.20.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_3.F_R1.fastq.gz HI.4096.008.Index_3.F_R1.fastq.gz", "fastq fastq", 2169884500.0, 21698845.0, "HI.4079.001.Index 3.F R1.fastq.gz", "0:100 1:0", "A:566808272;C:496620769;G:487930959;T:618144722;N:379778", 100, 0, null, null, 566808272, 496620769, 487930959, 618144722, 379778, "SRX2768772", "SRS2152480", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93678, null, 0.13131, null, 0.67635, null, 0.47972, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42203, "SRR5485635", "SRX2768771", "SRS2152482", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "G 4.0.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.0.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "G 4.0.2", "G 4.0.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_9.G_R1.fastq.gz HI.4096.008.Index_9.G_R1.fastq.gz", "fastq fastq", 2008051800.0, 20080518.0, "HI.4079.001.Index 9.G R1.fastq.gz", "0:100 1:0", "A:518304309;C:466602325;G:455957803;T:566834696;N:352667", 100, 0, null, null, 518304309, 466602325, 455957803, 566834696, 352667, "SRX2768771", "SRS2152482", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.94445, null, 0.12419, null, 0.68201, null, 0.46743, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42204, "SRR5485634", "SRX2768770", "SRS2152479", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "H 4.5.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.5.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "H 4.5.2", "H 4.5.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_8.H_R1.fastq.gz HI.4096.008.Index_8.H_R1.fastq.gz", "fastq fastq", 1908097900.0, 19080979.0, "HI.4079.001.Index 8.H R1.fastq.gz", "0:100 1:0", "A:494318032;C:441931870;G:431477592;T:540030651;N:339755", 100, 0, null, null, 494318032, 441931870, 431477592, 540030651, 339755, "SRX2768770", "SRS2152479", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.94216, null, 0.1306, null, 0.68195, null, 0.45834, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42205, "SRR5485633", "SRX2768769", "SRS2152477", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "I 4.20.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.20.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "I 4.20.2", "I 4.20.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_10.I_R1.fastq.gz HI.4096.008.Index_10.I_R1.fastq.gz", "fastq fastq", 2059931100.0, 20599311.0, "HI.4079.001.Index 10.I R1.fastq.gz", "0:100 1:0", "A:536731862;C:475769707;G:462890515;T:584183211;N:355805", 100, 0, null, null, 536731862, 475769707, 462890515, 584183211, 355805, "SRX2768769", "SRS2152477", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93561, null, 0.13393, null, 0.68225, null, 0.46489, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42206, "SRR5485632", "SRX2768768", "SRS2152478", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "J 4.0.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.0.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "J 4.0.14", "J 4.0.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_11.J_R1.fastq.gz HI.4096.008.Index_11.J_R1.fastq.gz", "fastq fastq", 2199504800.0, 21995048.0, "HI.4079.001.Index 11.J R1.fastq.gz", "0:100 1:0", "A:579625731;C:499663817;G:489173373;T:630657278;N:384601", 100, 0, null, null, 579625731, 499663817, 489173373, 630657278, 384601, "SRX2768768", "SRS2152478", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93523, null, 0.13836, null, 0.68655, null, 0.47839, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42207, "SRR5485631", "SRX2768767", "SRS2152475", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "K 4.5.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.5.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "K 4.5.14", "K 4.5.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_20.K_R1.fastq.gz HI.4096.008.Index_20.K_R1.fastq.gz", "fastq fastq", 2154282200.0, 21542822.0, "HI.4079.001.Index 20.K R1.fastq.gz", "0:100 1:0", "A:563358732;C:494058898;G:482596638;T:613890813;N:377119", 100, 0, null, null, 563358732, 494058898, 482596638, 613890813, 377119, "SRX2768767", "SRS2152475", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93863, null, 0.12932, null, 0.67801, null, 0.46426, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42208, "SRR5485630", "SRX2768766", "SRS2152476", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "L 4.20.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:4.20.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "L 4.20.14", "L 4.20.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4096.008.Index_22.L_R1.fastq.gz HI.4079.001.Index_22.L_R1.fastq.gz", "fastq fastq", 2702515700.0, 27025157.0, "HI.4079.001.Index 22.L R1.fastq.gz", "0:100 1:0", "A:708045960;C:615042366;G:603133757;T:775807969;N:485648", 100, 0, null, null, 708045960, 615042366, 603133757, 775807969, 485648, "SRX2768766", "SRS2152476", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93316, null, 0.14421, null, 0.68915, null, 0.47027, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2017-05-08", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42209, "SRR5485629", "SRX2768765", "SRS2152474", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "M 5.0.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.0.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "M 5.0.2", "M 5.0.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_25.M_R1.fastq.gz HI.4096.008.Index_25.M_R1.fastq.gz", "fastq fastq", 1999183400.0, 19991834.0, "HI.4079.001.Index 25.M R1.fastq.gz", "0:100 1:0", "A:526344986;C:456726468;G:447467581;T:568292150;N:352215", 100, 0, null, null, 526344986, 456726468, 447467581, 568292150, 352215, "SRX2768765", "SRS2152474", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.9374, null, 0.14185, null, 0.67665, null, 0.47249, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42210, "SRR5485628", "SRX2768764", "SRS2152473", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "N 5.5.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.5.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "N 5.5.2", "N 5.5.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_21.N_R1.fastq.gz HI.4096.008.Index_21.N_R1.fastq.gz", "fastq fastq", 2097386100.0, 20973861.0, "HI.4079.001.Index 21.N R1.fastq.gz", "0:100 1:0", "A:551586521;C:479609380;G:467572413;T:598246436;N:371350", 100, 0, null, null, 551586521, 479609380, 467572413, 598246436, 371350, "SRX2768764", "SRS2152473", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93984, null, 0.13949, null, 0.68219, null, 0.46921, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42211, "SRR5485627", "SRX2768763", "SRS2152472", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "O 5.20.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.20.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "O 5.20.2", "O 5.20.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_23.O_R1.fastq.gz HI.4096.008.Index_23.O_R1.fastq.gz", "fastq fastq", 2003835800.0, 20038358.0, "HI.4079.001.Index 23.O R1.fastq.gz", "0:100 1:0", "A:529075084;C:456810826;G:444441300;T:573155538;N:353052", 100, 0, null, null, 529075084, 456810826, 444441300, 573155538, 353052, "SRX2768763", "SRS2152472", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93635, null, 0.15287, null, 0.67712, null, 0.45807, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42212, "SRR5485626", "SRX2768762", "SRS2152471", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "P 5.0.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.0.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "P 5.0.14", "P 5.0.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_27.P_R1.fastq.gz HI.4096.008.Index_27.P_R1.fastq.gz", "fastq fastq", 1799355500.0, 17993555.0, "HI.4079.001.Index 27.P R1.fastq.gz", "0:100 1:0", "A:485156399;C:399414298;G:389730888;T:524733869;N:320046", 100, 0, null, null, 485156399, 399414298, 389730888, 524733869, 320046, "SRX2768762", "SRS2152471", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.92813, null, 0.15749, null, 0.67943, null, 0.47424, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42213, "SRR5485625", "SRX2768761", "SRS2152470", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "Q 5.5.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.5.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "Q 5.5.14", "Q 5.5.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_2.Q_R1.fastq.gz HI.4096.008.Index_2.Q_R1.fastq.gz", "fastq fastq", 2260494100.0, 22604941.0, "HI.4079.001.Index 2.Q R1.fastq.gz", "0:100 1:0", "A:602519260;C:506296484;G:495685951;T:655587703;N:404702", 100, 0, null, null, 602519260, 506296484, 495685951, 655587703, 404702, "SRX2768761", "SRS2152470", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.92524, null, 0.14979, null, 0.6859, null, 0.47957, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42214, "SRR5485624", "SRX2768760", "SRS2152469", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "R 5.20.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:5.20.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "R 5.20.14", "R 5.20.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_13.R_R1.fastq.gz HI.4096.008.Index_13.R_R1.fastq.gz", "fastq fastq", 1975297900.0, 19752979.0, "HI.4079.001.Index 13.R R1.fastq.gz", "0:100 1:0", "A:527732232;C:440160233;G:430962427;T:576091914;N:351094", 100, 0, null, null, 527732232, 440160233, 430962427, 576091914, 351094, "SRX2768760", "SRS2152469", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.92785, null, 0.15864, null, 0.6814, null, 0.47773, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42215, "SRR5485623", "SRX2768759", "SRS2152468", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "S 6.0.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:S 6.0.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "S 6.0.2", "S 6.0.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_6.S_R1.fastq.gz HI.4096.008.Index_6.S_R1.fastq.gz", "fastq fastq", 2690628500.0, 26906285.0, "HI.4079.001.Index 6.S R1.fastq.gz", "0:100 1:0", "A:713021693;C:609779787;G:594591832;T:772745072;N:490116", 100, 0, null, null, 713021693, 609779787, 594591832, 772745072, 490116, "SRX2768759", "SRS2152468", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93405, null, 0.15472, null, 0.68505, null, 0.45796, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42216, "SRR5485622", "SRX2768758", "SRS2152466", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "T 6.5.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.5.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "T 6.5.2", "T 6.5.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_15.T_R1.fastq.gz HI.4096.008.Index_15.T_R1.fastq.gz", "fastq fastq", 1949043500.0, 19490435.0, "HI.4079.001.Index 15.T R1.fastq.gz", "0:100 1:0", "A:515794596;C:441198348;G:430323928;T:561379111;N:347517", 100, 0, null, null, 515794596, 441198348, 430323928, 561379111, 347517, "SRX2768758", "SRS2152466", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93579, null, 0.16207, null, 0.68473, null, 0.44993, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42217, "SRR5485621", "SRX2768757", "SRS2152467", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "U 6.20.2", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.20.2|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "U 6.20.2", "U 6.20.2", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_7.U_R1.fastq.gz HI.4096.008.Index_7.U_R1.fastq.gz", "fastq fastq", 1754851900.0, 17548519.0, "HI.4079.001.Index 7.U R1.fastq.gz", "0:100 1:0", "A:464191451;C:397313933;G:387262108;T:505777499;N:306909", 100, 0, null, null, 464191451, 397313933, 387262108, 505777499, 306909, "SRX2768757", "SRS2152467", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.93016, null, 0.16163, null, 0.68329, null, 0.47088, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42218, "SRR5485620", "SRX2768756", "SRS2152463", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "V 6.0.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.0.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "V 6.0.14", "V 6.0.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_18.V_R1.fastq.gz HI.4096.008.Index_18.V_R1.fastq.gz", "fastq fastq", 2027423200.0, 20274232.0, "HI.4079.001.Index 18.V R1.fastq.gz", "0:100 1:0", "A:542440452;C:449399743;G:440389586;T:594839784;N:353635", 100, 0, null, null, 542440452, 449399743, 440389586, 594839784, 353635, "SRX2768756", "SRS2152463", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.92441, null, 0.16974, null, 0.6842, null, 0.48209, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42219, "SRR5485619", "SRX2768755", "SRS2152464", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "W 6.5.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.5.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "W 6.5.14", "W 6.5.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_14.W_R1.fastq.gz HI.4096.008.Index_14.W_R1.fastq.gz", "fastq fastq", 2139528300.0, 21395283.0, "HI.4079.001.Index 14.W R1.fastq.gz", "0:100 1:0", "A:569259910;C:478055273;G:469309420;T:622525486;N:378211", 100, 0, null, null, 569259910, 478055273, 469309420, 622525486, 378211, "SRX2768755", "SRS2152464", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.92551, null, 0.15358, null, 0.68136, null, 0.47093, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [42220, "SRR5485618", "SRX2768754", "SRS2152465", "SRP105410", "PRJNA384462", "Danio rerio Transcriptome or Gene expression", "PRJNA384462", "Whole Genome Sequencing", "5 dpf larval zebrafish Danio rerio were exposed to 0  5 and 20mg/L of virgin polyethylene microparticles in dechlorinated water for up to 14 days. Fish were maintained at 26C throughout the experiment and fed at libitum. Whole RNA was extracted from 4 replicates of 35 pooled embryos from each treatment at day 2 and day 14 post exposure with RNeasy kit QIAGEN. The NEB libraries generated from these extracted RNA were then sequenced on 2 Illumina HiSeq 2500 SR 100bp lanes.", null, null, null, null, "X 6.20.14", null, "ecotype:Growth Chamber|sex:male and female|tissue:Whole body|treatment:6.20.14|age:newborn|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "Danio rerio Raw sequence reads", "X 6.20.14", "X 6.20.14", "Illumina HiSeq read information to generate gene expression values", null, null, "WGS", "TRANSCRIPTOMIC", "RANDOM", "SINGLE", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP105410", null, null, "HI.4079.001.Index_16.X_R1.fastq.gz HI.4096.008.Index_16.X_R1.fastq.gz", "fastq fastq", 1768110400.0, 17681104.0, "HI.4079.001.Index 16.X R1.fastq.gz", "0:100 1:0", "A:472810124;C:392555880;G:382616900;T:519817796;N:309700", 100, 0, null, null, 472810124, 392555880, 382616900, 519817796, 309700, "SRX2768754", "SRS2152465", "SRA557480", "Brandon University|Biology", "Brandon University", 1, 0.92486, null, 0.16073, null, 0.69041, null, 0.48403, null, 100, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "random_priming", "unknown", "bulk", "unknown", "unknown", null, "Canada", "2018-09-11", "Undetermined", "Multi-stage", "Trunk", "Surface Structure"], [52250, "SRR9050625", "SRX5827016", "SRS4754830", "SRP198298", "PRJNA542704", "Thyroid hormone regulates distinct paths to maturation in pigment cell lineages", "GSE131136", "Transcriptome Analysis", "Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted  Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.", null, "pubmed:31140974;pubmed:33933422", null, "Neural crest derived cells from hypothyroid  juvenile zebrafish trunks  biological replicate 1", "GSM3764572", null, "tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:2135 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 11 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid", "Neural crest derived cells from hypothyroid  juvenile zebrafish trunks  biological replicate 1", "Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.", "sox10:Cre+ cells from post embryonic zebrafish trunk tissue", "Transgenic zebrafish  Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.", "10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.", "Zebrafish were maintained at 28.5 \u00b0C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia  rotifers enriched with TH free Algamac Aquafauna  and bloodworms.", "cell type:2135 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Fish range in stage from 11 SSL stage zebrafish. Thyroid ablation was performed at 4 dpf with metronidazole treatment.|treatment:Hypothyroid", "GSM3764572", "GSM3764572: Neural crest derived cells from hypothyroid  juvenile zebrafish trunks  biological replicate 1; Danio rerio; RNA Seq", "GSM3764572", null, "1", "10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP198298", null, "dangling references:treat as unmapped", "hypo7_possorted_genome_bam.bam", "10X Genomics bam file", 5078170983.0, 89090719.0, "GSM3764572 r1", "0:57", "A:1526791201;C:989860604;G:1192544480;T:1366270035;N:2704663", 57, null, null, null, 1526791201, 989860604, 1192544480, 1366270035, 2704663, "SRX5827016", "SRS4754830", "SRA886020", "GEO", "Biology, University of Virginia", 1, 0.92899, null, 0.25348, null, 0.83571, null, 0.48794, null, 57, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-05-13", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [52256, "SRR9050619", "SRX5827010", "SRS4754824", "SRP198298", "PRJNA542704", "Thyroid hormone regulates distinct paths to maturation in pigment cell lineages", "GSE131136", "Transcriptome Analysis", "Early and post embryonic neural crest derived lineages in the zebrafish trunk in response to thyroid hormone modulation Overall design: Single cell RNA seq experiments were performed on the 10X Genomics platform from FAC sorted  Sox10:CRE positive cells from 5dpf and post embryonic zebrafish trunks with and without xxx hormone.", null, "pubmed:31140974;pubmed:33933422", null, "Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 1", "GSM3764566", null, "tissue:sox10:Cre+ cells from post embryonic zebrafish trunk tissue|cell type:2168 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Zebrafish were stage 11 SSL stage juvenile.|treatment:Euthyroid", "Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 1", "Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger. All samples were aggregated using the aggregate option in cellranger to normalize mean number of reads per cell across 10X libraries. Genome build: GRCz11 Supplementary files format and content: Expression matrix files and BAM files were generated using cellranger 10X genomics version 2.0.2 as described by the manufacturer using the commands cellranger demux and cellranger count. UMI count matrices representing the filtered set of barcodes representing cells were used as determined by cellranger.  Expression matrices are output by cellranger and are in Matrix Market Exchange format and the gene and cell barcode name files that accompany these file are provided as TSV files.", "sox10:Cre+ cells from post embryonic zebrafish trunk tissue", "Transgenic zebrafish  Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  were treated either metronidazole 10mM or a vehicle control DMSO at 4dpf. Trunks or skins were collected at a stage range of 7.2 10.4 SSL or 5 dpf as indicated in the sample name. Tissue was dissociated into a single cell suspension and FAC sorted for the presence of mCherry. Then cells were washed and loaded into the 10X chromium chip according to manufacturer recommendations.", "10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.", "Zebrafish were maintained at 28.5 \u00b0C under 14:10 light:dark cycles. All thyroid ablated Mtz treated and control DMSO treated Tgtg:nVenus v2a nfnB fish were kept under TH free conditions and were fed only Artemia  rotifers enriched with TH free Algamac Aquafauna  and bloodworms.", "cell type:2168 cells from Tgsox10:Cre; ubi:switch; tg:nVenus 2a nfnB  FAC sorted mCherry+ cells from trunks. Zebrafish were stage 11 SSL stage juvenile.|treatment:Euthyroid", "GSM3764566", "GSM3764566: Neural crest derived cells from euthyroid  post embryonic zebrafish trunks  biological replicate 1; Danio rerio; RNA Seq", "GSM3764566", null, "1", "10X genomics single cell gene expression V2 protocol following manufacturer recommendations. 10X genomics single cell gene expression V2 protocol following manufacturer recommendations.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP198298", null, "dangling references:treat as unmapped", "eu6_possorted_genome_bam.bam", "10X Genomics bam file", 5005233954.0, 87811122.0, "GSM3764566 r1", "0:57", "A:1531421605;C:966957285;G:1151579626;T:1352667292;N:2608146", 57, null, null, null, 1531421605, 966957285, 1151579626, 1352667292, 2608146, "SRX5827010", "SRS4754824", "SRA886020", "GEO", "Biology, University of Virginia", 1, 0.92288, null, 0.25231, null, 0.83479, null, 0.5014, null, 57, null, "B", null, "usable mapping rate", "illumina", "nextseq", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2019-05-13", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [66727, "SRR16494150", "SRX12697149", "SRS10647152", "SRP342232", "PRJNA772880", "Bisphenol S affects zebrafish RNA seq analysis", "PRJNA772880", "Other", "RNAseq data of 48 hpf zebrafish under bisphenol S", null, null, "BPS1 3", "RNA seq of zebrafish at 48 hpf in DMSO exposed", "FKRO210105138 1A", null, "isolate:AB type|ecotype:AB type|age:1 year|dev stage:48 hpf|sex:not applicable|tissue:all body|biomaterial provider:ecotoxicology of OUC|ID:replicate=6|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish at 48 hpf : 1g/L bisohenol exposed", "FRAS210076288 1r", "FRAS210076288 1r", "The first cDNA strand was synthesized in the m MulV reverse transcriptase system  and then the RNA strand was degraded by RNaseH. The second strand of cDNA was synthesized in the DNA polymerase I system. AMPure XPbeads were used to screen the cDNA from 370 bp to 420 bp. PCR amplification was performed and PCR products were purified again with AMPure XP Beads to obtain the library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP342232", null, null, "BPS1_3_1.fq.gz BPS1_3_2.fq.gz", "fastq fastq", 7167849600.0, 23892832.0, "BPS1 3 1.fq.gz", "0:150 1:150", "A:1918014367;C:1678861019;G:1677677143;T:1893251281;N:45790", 150, 150, null, null, 1918014367, 1678861019, 1677677143, 1893251281, 45790, "SRX12697149", "SRS10647152", "SRA1313827", "Ocean University of China|College of Marine Life Sciences", "Ocean University of China", 2, 0.95027, 0.95031, 0.10013, 0.10018, 0.67789, 0.67771, 0.45849, 0.45672, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-10-20", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [66728, "SRR16494151", "SRX12697148", "SRS10647151", "SRP342232", "PRJNA772880", "Bisphenol S affects zebrafish RNA seq analysis", "PRJNA772880", "Other", "RNAseq data of 48 hpf zebrafish under bisphenol S", null, null, "BPS1 2", "RNA seq of zebrafish at 48 hpf in DMSO exposed", "FKRO210105137 1A", null, "isolate:AB type|ecotype:AB type|age:1 year|dev stage:48 hpf|sex:not applicable|tissue:all body|biomaterial provider:ecotoxicology of OUC|ID:replicate=5|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish at 48 hpf : 1g/L bisohenol exposed", "FRAS210076287 1r", "FRAS210076287 1r", "The first cDNA strand was synthesized in the m MulV reverse transcriptase system  and then the RNA strand was degraded by RNaseH. The second strand of cDNA was synthesized in the DNA polymerase I system. AMPure XPbeads were used to screen the cDNA from 370 bp to 420 bp. PCR amplification was performed and PCR products were purified again with AMPure XP Beads to obtain the library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP342232", null, null, "BPS1_2_1.fq.gz BPS1_2_2.fq.gz", "fastq fastq", 7612619700.0, 25375399.0, "BPS1 2 1.fq.gz", "0:150 1:150", "A:2031729658;C:1792968404;G:1787711984;T:1999989075;N:220579", 150, 150, null, null, 2031729658, 1792968404, 1787711984, 1999989075, 220579, "SRX12697148", "SRS10647151", "SRA1313827", "Ocean University of China|College of Marine Life Sciences", "Ocean University of China", 2, 0.95101, 0.95113, 0.09524, 0.09456, 0.68274, 0.68318, 0.45837, 0.45319, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-10-20", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [66729, "SRR16494152", "SRX12697147", "SRS10647150", "SRP342232", "PRJNA772880", "Bisphenol S affects zebrafish RNA seq analysis", "PRJNA772880", "Other", "RNAseq data of 48 hpf zebrafish under bisphenol S", null, null, "BPS1 1", "RNA seq of zebrafish at 48 hpf in DMSO exposed", "FKRO210105136 1A", null, "isolate:AB type|ecotype:AB type|age:1 year|dev stage:48 hpf|sex:not applicable|tissue:all body|biomaterial provider:ecotoxicology of OUC|ID:replicate=4|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish at 48 hpf : 1g/L bisohenol exposed", "FRAS210076286 1r", "FRAS210076286 1r", "The first cDNA strand was synthesized in the m MulV reverse transcriptase system  and then the RNA strand was degraded by RNaseH. The second strand of cDNA was synthesized in the DNA polymerase I system. AMPure XPbeads were used to screen the cDNA from 370 bp to 420 bp. PCR amplification was performed and PCR products were purified again with AMPure XP Beads to obtain the library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP342232", null, null, "BPS1_1_1.fq.gz BPS1_1_2.fq.gz", "fastq fastq", 6244935600.0, 20816452.0, "BPS1 1 1.fq.gz", "0:150 1:150", "A:1675323145;C:1456410435;G:1458522814;T:1654433698;N:245508", 150, 150, null, null, 1675323145, 1456410435, 1458522814, 1654433698, 245508, "SRX12697147", "SRS10647150", "SRA1313827", "Ocean University of China|College of Marine Life Sciences", "Ocean University of China", 2, 0.94597, 0.94597, 0.10252, 0.1028, 0.67913, 0.67963, 0.4519, 0.45424, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-10-20", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [66730, "SRR16494153", "SRX12697146", "SRS10647149", "SRP342232", "PRJNA772880", "Bisphenol S affects zebrafish RNA seq analysis", "PRJNA772880", "Other", "RNAseq data of 48 hpf zebrafish under bisphenol S", null, null, "DMSO 3", "RNA seq of zebrafish at 48 hpf in DMSO exposed", "FKRO210105135 1A", null, "isolate:AB type|ecotype:AB type|age:1 year|dev stage:48 hpf|sex:not applicable|tissue:all body|biomaterial provider:ecotoxicology of OUC|ID:replicate=3|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish at 48 hpf : DMSO exposed", "FRAS210076285 1r", "FRAS210076285 1r", "The first cDNA strand was synthesized in the m MulV reverse transcriptase system  and then the RNA strand was degraded by RNaseH. The second strand of cDNA was synthesized in the DNA polymerase I system. AMPure XPbeads were used to screen the cDNA from 370 bp to 420 bp. PCR amplification was performed and PCR products were purified again with AMPure XP Beads to obtain the library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP342232", null, null, "DMSO_3_1.fq.gz DMSO_3_2.fq.gz", "fastq fastq", 6977113200.0, 23257044.0, "DMSO 3 1.fq.gz", "0:150 1:150", "A:1886115659;C:1619020544;G:1612888187;T:1858808303;N:280507", 150, 150, null, null, 1886115659, 1619020544, 1612888187, 1858808303, 280507, "SRX12697146", "SRS10647149", "SRA1313827", "Ocean University of China|College of Marine Life Sciences", "Ocean University of China", 2, 0.94817, 0.94818, 0.10571, 0.10532, 0.67957, 0.6802, 0.46251, 0.46156, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-10-20", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [66731, "SRR16494154", "SRX12697145", "SRS10647148", "SRP342232", "PRJNA772880", "Bisphenol S affects zebrafish RNA seq analysis", "PRJNA772880", "Other", "RNAseq data of 48 hpf zebrafish under bisphenol S", null, null, "DMSO 2", "RNA seq of zebrafish at 48 hpf in DMSO exposed", "FKRO210105134 1A", null, "isolate:AB type|ecotype:AB type|age:1 year|dev stage:48 hpf|sex:not applicable|tissue:all body|biomaterial provider:ecotoxicology of OUC|ID:replicate=2|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish at 48 hpf : DMSO exposed", "FRAS210076284 1r", "FRAS210076284 1r", "The first cDNA strand was synthesized in the m MulV reverse transcriptase system  and then the RNA strand was degraded by RNaseH. The second strand of cDNA was synthesized in the DNA polymerase I system. AMPure XPbeads were used to screen the cDNA from 370 bp to 420 bp. PCR amplification was performed and PCR products were purified again with AMPure XP Beads to obtain the library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP342232", null, null, "DMSO_2_1.fq.gz DMSO_2_2.fq.gz", "fastq fastq", 6084760800.0, 20282536.0, "DMSO 2 1.fq.gz", "0:150 1:150", "A:1662685386;C:1398235089;G:1387347206;T:1636254391;N:238728", 150, 150, null, null, 1662685386, 1398235089, 1387347206, 1636254391, 238728, "SRX12697145", "SRS10647148", "SRA1313827", "Ocean University of China|College of Marine Life Sciences", "Ocean University of China", 2, 0.94513, 0.94552, 0.12007, 0.12016, 0.67732, 0.67698, 0.46577, 0.46663, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-10-20", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [66732, "SRR16494155", "SRX12697144", "SRS10647147", "SRP342232", "PRJNA772880", "Bisphenol S affects zebrafish RNA seq analysis", "PRJNA772880", "Other", "RNAseq data of 48 hpf zebrafish under bisphenol S", null, null, "DMSO 1", "RNA seq of zebrafish at 48 hpf in DMSO exposed", "FKRO210105133 1A", null, "isolate:AB type|ecotype:AB type|age:1 year|dev stage:48 hpf|sex:not applicable|tissue:all body|biomaterial provider:ecotoxicology of OUC|ID:replicate=1|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA seq of zebrafish at 48 hpf : DMSO exposed", "FRAS210076283 1r", "FRAS210076283 1r", "The first cDNA strand was synthesized in the m MulV reverse transcriptase system  and then the RNA strand was degraded by RNaseH. The second strand of cDNA was synthesized in the DNA polymerase I system. AMPure XPbeads were used to screen the cDNA from 370 bp to 420 bp. PCR amplification was performed and PCR products were purified again with AMPure XP Beads to obtain the library.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP342232", null, null, "DMSO_1_1.fq.gz DMSO_1_2.fq.gz", "fastq fastq", 7313502000.0, 24378340.0, "DMSO 1 1.fq.gz", "0:150 1:150", "A:1980180330;C:1695610385;G:1686058673;T:1951359106;N:293506", 150, 150, null, null, 1980180330, 1695610385, 1686058673, 1951359106, 293506, "SRX12697144", "SRS10647147", "SRA1313827", "Ocean University of China|College of Marine Life Sciences", "Ocean University of China", 2, 0.94872, 0.94801, 0.10719, 0.10597, 0.68221, 0.68162, 0.47058, 0.46764, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "China", "2021-10-20", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [72477, "SRR22577926", "SRX18540948", "SRS16005333", "SRP412040", "PRJNA910181", "Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos", "GSE220546", "Transcriptome Analysis", "Heat alters biology from molecular to ecological levels  but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here  we provide a comprehensive picture of the molecular signatures of this process  by integrating multiomic and phenotypic data. In individual zebrafish embryos  repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response  extracellular signalling  glycosaminoglycan/keratan sulphate  and lipid metabolism. Consequently  non heat exposed receivers exposed to stress metabolites only experienced accelerated catch up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most  mediated by apelin signalling. Our results prove the concept of indirect heat induced stress propagation towards naive receivers  inducing phenotypes comparable to those resulting from direct heat exposure  but utilising distinct molecular pathways. Group exposing a non laboratory zebrafish line  we independently confirm that the glycosaminoglycan biosynthesis related gene chs1  and the mucus glycoprotein gene prg4a  functionally connected to the candidate stress metabolite classes sugars and phosphocholine  are differentially expressed in receivers. This hints at the production of Schreckstoff like cues in receivers  leading to further stress propagation within groups  which may have ecological and animal welfare implications for aquatic populations in a changing climate. Overall design: Zebrafish embryos were exposed for 24 hours to thermal stress TS and stress metabolites SM released by heat stressed zebrafish embryos  in a two way factorial design TSxSM  yielding four experimental treatments: fresh medium at 27\u00b0C control C  fresh medium with thermal stress TS  medium containing stress metabolites at 27\u00b0C SM  and medium containing stress metabolites with thermal stress TS+SM. Each treatment contains n = 3 biological replicates  each representing the pooled gene expression from 20 individual embryos.", null, "pubmed:37228511", null, "SM3  sample RNA42", "GSM6806702", null, "source name:1 dpf whole body embryos|tissue:1 dpf whole body embryos|genotype:Wild type Line: AB|time:1 dpf group:SM|treatment:Stress Metabolites at 27C", "SM3  sample RNA42", "The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1. Reads were filtered and trimmed using fastp v0.23.1  to remove low quality reads  polyG  polyX  and Illumina adapter sequences. Default parameters were used along with   dup calc accuracy 3   trim poly g   trim poly x Reads were aligned to the zebrafish reference genome using STAR v2.6.1 Reads were counted by gene using STAR v2.6.1   runMode alignReads   quantMode TranscriptomeSAM GeneCounts   outSAMtype BAM SortedByCoordinate   outSAMunmapped None   outSAMattributes Standard Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2. Assembly: primary genome assembly GRCz11.104 http://ftp.ensembl.org/pub/release 104/fasta/danio rerio/dna/Danio rerio.GRCz11.dna sm.primary assembly.fa.gz and http://ftp.ensembl.org/pub/release 104/gtf/danio rerio/Danio rerio.GRCz11.104.gtf.gz Supplementary files format and content: The files with \" ReadsPerGenes.fastp.noD.tab\" name extensions are read counts per gene obtained from STAR  which were used in DESeq2 for differential expression analysis.", "1 dpf whole body embryos", "Two temperature protocols were used  either i a control constant temperature of 27\u00b0C  or ii  thermal stress protocol consisting of repeated heat stress with temperature fluctuations  between 27  29  32  29  and 27\u00b0C  with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium fresh medium free of metabolites or stress medium with stress metabolites  SM and incubated with their temperature protocols for 24 hours  from 11 am once they reached the stage of 2 3.3 hpf to 11 am on the next day. At 1 dpf  i.e. post 24 hours of experimental treatment  embryos were sampled by pools of 20 per condition  and snap frozen at  80\u00b0C before total RNA extraction.", "Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations  and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.", "Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish wild type AB maintained at 27\u00b0C  with 14:10 light:dark cycles.  Embryos were incubated in individual 0.2 mL PCR tubes one embryo per tube containing 200 \u03bcL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.", "tissue:1 dpf whole body embryos|genotype:Wild type Line: AB|time:1 dpf group:SM|treatment:Stress Metabolites at 27C", "GSM6806702", "GSM6806702: SM3  sample RNA42; Danio rerio; RNA Seq", "GSM6806702 r1", "GSM6806702", "1", "Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations  and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP412040", null, "loader:fastq load.py", "211020_A00291_0393_AHM5V2DRXY_1_12030WK0041L01_1.fastq.gz 211020_A00291_0393_AHM5V2DRXY_1_12030WK0041L01_2.fastq.gz", "fastq fastq", 3476829400.0, 34768294.0, "GSM6806702 r1", "0:50 1:50", "A:938556753;C:788469231;G:822145048;T:927563690;N:94678", 50, 50, null, null, 938556753, 788469231, 822145048, 927563690, 94678, "SRX18540948", "SRS16005333", "SRA1555908", "Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull", "Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull", 2, 0.95691, 0.96146, 0.10137, 0.10597, 0.73734, 0.73996, 0.51422, 0.51046, 50, 50, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2022-12-08", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [72478, "SRR22577927", "SRX18540947", "SRS16005332", "SRP412040", "PRJNA910181", "Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos", "GSE220546", "Transcriptome Analysis", "Heat alters biology from molecular to ecological levels  but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here  we provide a comprehensive picture of the molecular signatures of this process  by integrating multiomic and phenotypic data. In individual zebrafish embryos  repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response  extracellular signalling  glycosaminoglycan/keratan sulphate  and lipid metabolism. Consequently  non heat exposed receivers exposed to stress metabolites only experienced accelerated catch up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most  mediated by apelin signalling. Our results prove the concept of indirect heat induced stress propagation towards naive receivers  inducing phenotypes comparable to those resulting from direct heat exposure  but utilising distinct molecular pathways. Group exposing a non laboratory zebrafish line  we independently confirm that the glycosaminoglycan biosynthesis related gene chs1  and the mucus glycoprotein gene prg4a  functionally connected to the candidate stress metabolite classes sugars and phosphocholine  are differentially expressed in receivers. This hints at the production of Schreckstoff like cues in receivers  leading to further stress propagation within groups  which may have ecological and animal welfare implications for aquatic populations in a changing climate. Overall design: Zebrafish embryos were exposed for 24 hours to thermal stress TS and stress metabolites SM released by heat stressed zebrafish embryos  in a two way factorial design TSxSM  yielding four experimental treatments: fresh medium at 27\u00b0C control C  fresh medium with thermal stress TS  medium containing stress metabolites at 27\u00b0C SM  and medium containing stress metabolites with thermal stress TS+SM. Each treatment contains n = 3 biological replicates  each representing the pooled gene expression from 20 individual embryos.", null, "pubmed:37228511", null, "C3  sample RNA37", "GSM6806701", null, "source name:1 dpf whole body embryos|tissue:1 dpf whole body embryos|genotype:Wild type Line: AB|time:1 dpf group:C|treatment:Control fresh medium at 27C", "C3  sample RNA37", "The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1. Reads were filtered and trimmed using fastp v0.23.1  to remove low quality reads  polyG  polyX  and Illumina adapter sequences. Default parameters were used along with   dup calc accuracy 3   trim poly g   trim poly x Reads were aligned to the zebrafish reference genome using STAR v2.6.1 Reads were counted by gene using STAR v2.6.1   runMode alignReads   quantMode TranscriptomeSAM GeneCounts   outSAMtype BAM SortedByCoordinate   outSAMunmapped None   outSAMattributes Standard Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2. Assembly: primary genome assembly GRCz11.104 http://ftp.ensembl.org/pub/release 104/fasta/danio rerio/dna/Danio rerio.GRCz11.dna sm.primary assembly.fa.gz and http://ftp.ensembl.org/pub/release 104/gtf/danio rerio/Danio rerio.GRCz11.104.gtf.gz Supplementary files format and content: The files with \" ReadsPerGenes.fastp.noD.tab\" name extensions are read counts per gene obtained from STAR  which were used in DESeq2 for differential expression analysis.", "1 dpf whole body embryos", "Two temperature protocols were used  either i a control constant temperature of 27\u00b0C  or ii  thermal stress protocol consisting of repeated heat stress with temperature fluctuations  between 27  29  32  29  and 27\u00b0C  with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium fresh medium free of metabolites or stress medium with stress metabolites  SM and incubated with their temperature protocols for 24 hours  from 11 am once they reached the stage of 2 3.3 hpf to 11 am on the next day. At 1 dpf  i.e. post 24 hours of experimental treatment  embryos were sampled by pools of 20 per condition  and snap frozen at  80\u00b0C before total RNA extraction.", "Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations  and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.", "Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish wild type AB maintained at 27\u00b0C  with 14:10 light:dark cycles.  Embryos were incubated in individual 0.2 mL PCR tubes one embryo per tube containing 200 \u03bcL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.", "tissue:1 dpf whole body embryos|genotype:Wild type Line: AB|time:1 dpf group:C|treatment:Control fresh medium at 27C", "GSM6806701", "GSM6806701: C3  sample RNA37; Danio rerio; RNA Seq", "GSM6806701 r1", "GSM6806701", "1", "Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations  and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP412040", null, "loader:fastq load.py", "211020_A00291_0393_AHM5V2DRXY_1_12030WK0012L01_1.fastq.gz 211020_A00291_0393_AHM5V2DRXY_1_12030WK0012L01_2.fastq.gz", "fastq fastq", 3115511600.0, 31155116.0, "GSM6806701 r1", "0:50 1:50", "A:818169661;C:736800852;G:743832124;T:816625526;N:83437", 50, 50, null, null, 818169661, 736800852, 743832124, 816625526, 83437, "SRX18540947", "SRS16005332", "SRA1555908", "Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull", "Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull", 2, 0.95909, 0.9622, 0.08549, 0.08662, 0.72174, 0.72216, 0.47764, 0.47929, 50, 50, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2022-12-08", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [72479, "SRR22577928", "SRX18540946", "SRS16005331", "SRP412040", "PRJNA910181", "Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos", "GSE220546", "Transcriptome Analysis", "Heat alters biology from molecular to ecological levels  but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here  we provide a comprehensive picture of the molecular signatures of this process  by integrating multiomic and phenotypic data. In individual zebrafish embryos  repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response  extracellular signalling  glycosaminoglycan/keratan sulphate  and lipid metabolism. Consequently  non heat exposed receivers exposed to stress metabolites only experienced accelerated catch up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most  mediated by apelin signalling. Our results prove the concept of indirect heat induced stress propagation towards naive receivers  inducing phenotypes comparable to those resulting from direct heat exposure  but utilising distinct molecular pathways. Group exposing a non laboratory zebrafish line  we independently confirm that the glycosaminoglycan biosynthesis related gene chs1  and the mucus glycoprotein gene prg4a  functionally connected to the candidate stress metabolite classes sugars and phosphocholine  are differentially expressed in receivers. This hints at the production of Schreckstoff like cues in receivers  leading to further stress propagation within groups  which may have ecological and animal welfare implications for aquatic populations in a changing climate. Overall design: Zebrafish embryos were exposed for 24 hours to thermal stress TS and stress metabolites SM released by heat stressed zebrafish embryos  in a two way factorial design TSxSM  yielding four experimental treatments: fresh medium at 27\u00b0C control C  fresh medium with thermal stress TS  medium containing stress metabolites at 27\u00b0C SM  and medium containing stress metabolites with thermal stress TS+SM. Each treatment contains n = 3 biological replicates  each representing the pooled gene expression from 20 individual embryos.", null, "pubmed:37228511", null, "TS3  sample RNA36", "GSM6806700", null, "source name:1 dpf whole body embryos|tissue:1 dpf whole body embryos|genotype:Wild type Line: AB|time:1 dpf group:TS|treatment:Fresh medium with repeated heat stress", "TS3  sample RNA36", "The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1. Reads were filtered and trimmed using fastp v0.23.1  to remove low quality reads  polyG  polyX  and Illumina adapter sequences. Default parameters were used along with   dup calc accuracy 3   trim poly g   trim poly x Reads were aligned to the zebrafish reference genome using STAR v2.6.1 Reads were counted by gene using STAR v2.6.1   runMode alignReads   quantMode TranscriptomeSAM GeneCounts   outSAMtype BAM SortedByCoordinate   outSAMunmapped None   outSAMattributes Standard Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2. Assembly: primary genome assembly GRCz11.104 http://ftp.ensembl.org/pub/release 104/fasta/danio rerio/dna/Danio rerio.GRCz11.dna sm.primary assembly.fa.gz and http://ftp.ensembl.org/pub/release 104/gtf/danio rerio/Danio rerio.GRCz11.104.gtf.gz Supplementary files format and content: The files with \" ReadsPerGenes.fastp.noD.tab\" name extensions are read counts per gene obtained from STAR  which were used in DESeq2 for differential expression analysis.", "1 dpf whole body embryos", "Two temperature protocols were used  either i a control constant temperature of 27\u00b0C  or ii  thermal stress protocol consisting of repeated heat stress with temperature fluctuations  between 27  29  32  29  and 27\u00b0C  with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium fresh medium free of metabolites or stress medium with stress metabolites  SM and incubated with their temperature protocols for 24 hours  from 11 am once they reached the stage of 2 3.3 hpf to 11 am on the next day. At 1 dpf  i.e. post 24 hours of experimental treatment  embryos were sampled by pools of 20 per condition  and snap frozen at  80\u00b0C before total RNA extraction.", "Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations  and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.", "Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish wild type AB maintained at 27\u00b0C  with 14:10 light:dark cycles.  Embryos were incubated in individual 0.2 mL PCR tubes one embryo per tube containing 200 \u03bcL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.", "tissue:1 dpf whole body embryos|genotype:Wild type Line: AB|time:1 dpf group:TS|treatment:Fresh medium with repeated heat stress", "GSM6806700", "GSM6806700: TS3  sample RNA36; Danio rerio; RNA Seq", "GSM6806700 r1", "GSM6806700", "1", "Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations  and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP412040", null, "loader:fastq load.py", "211020_A00291_0393_AHM5V2DRXY_1_12030WK0011L01_1.fastq.gz 211020_A00291_0393_AHM5V2DRXY_1_12030WK0011L01_2.fastq.gz", "fastq fastq", 4015833000.0, 40158330.0, "GSM6806700 r1", "0:50 1:50", "A:1048452902;C:957562374;G:965130701;T:1044578904;N:108119", 50, 50, null, null, 1048452902, 957562374, 965130701, 1044578904, 108119, "SRX18540946", "SRS16005331", "SRA1555908", "Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull", "Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull", 2, 0.96228, 0.9654, 0.07673, 0.07871, 0.71565, 0.71699, 0.47598, 0.48696, 50, 50, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2022-12-08", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [72480, "SRR22577929", "SRX18540945", "SRS16005330", "SRP412040", "PRJNA910181", "Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos", "GSE220546", "Transcriptome Analysis", "Heat alters biology from molecular to ecological levels  but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here  we provide a comprehensive picture of the molecular signatures of this process  by integrating multiomic and phenotypic data. In individual zebrafish embryos  repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response  extracellular signalling  glycosaminoglycan/keratan sulphate  and lipid metabolism. Consequently  non heat exposed receivers exposed to stress metabolites only experienced accelerated catch up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most  mediated by apelin signalling. Our results prove the concept of indirect heat induced stress propagation towards naive receivers  inducing phenotypes comparable to those resulting from direct heat exposure  but utilising distinct molecular pathways. Group exposing a non laboratory zebrafish line  we independently confirm that the glycosaminoglycan biosynthesis related gene chs1  and the mucus glycoprotein gene prg4a  functionally connected to the candidate stress metabolite classes sugars and phosphocholine  are differentially expressed in receivers. This hints at the production of Schreckstoff like cues in receivers  leading to further stress propagation within groups  which may have ecological and animal welfare implications for aquatic populations in a changing climate. Overall design: Zebrafish embryos were exposed for 24 hours to thermal stress TS and stress metabolites SM released by heat stressed zebrafish embryos  in a two way factorial design TSxSM  yielding four experimental treatments: fresh medium at 27\u00b0C control C  fresh medium with thermal stress TS  medium containing stress metabolites at 27\u00b0C SM  and medium containing stress metabolites with thermal stress TS+SM. Each treatment contains n = 3 biological replicates  each representing the pooled gene expression from 20 individual embryos.", null, "pubmed:37228511", null, "TS+SM3  sample RNA35", "GSM6806699", null, "source name:1 dpf whole body embryos|tissue:1 dpf whole body embryos|genotype:Wild type Line: AB|time:1 dpf group:TS+SM|treatment:Stress Metabolites with repeated heat stress", "TS+SM3  sample RNA35", "The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1. Reads were filtered and trimmed using fastp v0.23.1  to remove low quality reads  polyG  polyX  and Illumina adapter sequences. Default parameters were used along with   dup calc accuracy 3   trim poly g   trim poly x Reads were aligned to the zebrafish reference genome using STAR v2.6.1 Reads were counted by gene using STAR v2.6.1   runMode alignReads   quantMode TranscriptomeSAM GeneCounts   outSAMtype BAM SortedByCoordinate   outSAMunmapped None   outSAMattributes Standard Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2. Assembly: primary genome assembly GRCz11.104 http://ftp.ensembl.org/pub/release 104/fasta/danio rerio/dna/Danio rerio.GRCz11.dna sm.primary assembly.fa.gz and http://ftp.ensembl.org/pub/release 104/gtf/danio rerio/Danio rerio.GRCz11.104.gtf.gz Supplementary files format and content: The files with \" ReadsPerGenes.fastp.noD.tab\" name extensions are read counts per gene obtained from STAR  which were used in DESeq2 for differential expression analysis.", "1 dpf whole body embryos", "Two temperature protocols were used  either i a control constant temperature of 27\u00b0C  or ii  thermal stress protocol consisting of repeated heat stress with temperature fluctuations  between 27  29  32  29  and 27\u00b0C  with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium fresh medium free of metabolites or stress medium with stress metabolites  SM and incubated with their temperature protocols for 24 hours  from 11 am once they reached the stage of 2 3.3 hpf to 11 am on the next day. At 1 dpf  i.e. post 24 hours of experimental treatment  embryos were sampled by pools of 20 per condition  and snap frozen at  80\u00b0C before total RNA extraction.", "Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations  and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.", "Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish wild type AB maintained at 27\u00b0C  with 14:10 light:dark cycles.  Embryos were incubated in individual 0.2 mL PCR tubes one embryo per tube containing 200 \u03bcL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.", "tissue:1 dpf whole body embryos|genotype:Wild type Line: AB|time:1 dpf group:TS+SM|treatment:Stress Metabolites with repeated heat stress", "GSM6806699", "GSM6806699: TS+SM3  sample RNA35; Danio rerio; RNA Seq", "GSM6806699 r1", "GSM6806699", "1", "Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations  and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP412040", null, "loader:fastq load.py", "211020_A00291_0393_AHM5V2DRXY_1_12030WK0010L01_1.fastq.gz 211020_A00291_0393_AHM5V2DRXY_1_12030WK0010L01_2.fastq.gz", "fastq fastq", 2689361200.0, 26893612.0, "GSM6806699 r1", "0:50 1:50", "A:714380354;C:630443184;G:634772606;T:709693436;N:71620", 50, 50, null, null, 714380354, 630443184, 634772606, 709693436, 71620, "SRX18540945", "SRS16005330", "SRA1555908", "Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull", "Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull", 2, 0.95508, 0.96036, 0.11483, 0.11626, 0.72464, 0.72512, 0.50789, 0.50728, 50, 50, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2022-12-08", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [72481, "SRR22577933", "SRX18540944", "SRS16005329", "SRP412040", "PRJNA910181", "Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos", "GSE220546", "Transcriptome Analysis", "Heat alters biology from molecular to ecological levels  but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here  we provide a comprehensive picture of the molecular signatures of this process  by integrating multiomic and phenotypic data. In individual zebrafish embryos  repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response  extracellular signalling  glycosaminoglycan/keratan sulphate  and lipid metabolism. Consequently  non heat exposed receivers exposed to stress metabolites only experienced accelerated catch up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most  mediated by apelin signalling. Our results prove the concept of indirect heat induced stress propagation towards naive receivers  inducing phenotypes comparable to those resulting from direct heat exposure  but utilising distinct molecular pathways. Group exposing a non laboratory zebrafish line  we independently confirm that the glycosaminoglycan biosynthesis related gene chs1  and the mucus glycoprotein gene prg4a  functionally connected to the candidate stress metabolite classes sugars and phosphocholine  are differentially expressed in receivers. This hints at the production of Schreckstoff like cues in receivers  leading to further stress propagation within groups  which may have ecological and animal welfare implications for aquatic populations in a changing climate. Overall design: Zebrafish embryos were exposed for 24 hours to thermal stress TS and stress metabolites SM released by heat stressed zebrafish embryos  in a two way factorial design TSxSM  yielding four experimental treatments: fresh medium at 27\u00b0C control C  fresh medium with thermal stress TS  medium containing stress metabolites at 27\u00b0C SM  and medium containing stress metabolites with thermal stress TS+SM. Each treatment contains n = 3 biological replicates  each representing the pooled gene expression from 20 individual embryos.", null, "pubmed:37228511", null, "C2  sample RNA12", "GSM6806698", null, "source name:1 dpf whole body embryos|tissue:1 dpf whole body embryos|genotype:Wild type Line: AB|time:1 dpf group:C|treatment:Control fresh medium at 27C", "C2  sample RNA12", "The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1. Reads were filtered and trimmed using fastp v0.23.1  to remove low quality reads  polyG  polyX  and Illumina adapter sequences. Default parameters were used along with   dup calc accuracy 3   trim poly g   trim poly x Reads were aligned to the zebrafish reference genome using STAR v2.6.1 Reads were counted by gene using STAR v2.6.1   runMode alignReads   quantMode TranscriptomeSAM GeneCounts   outSAMtype BAM SortedByCoordinate   outSAMunmapped None   outSAMattributes Standard Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2. Assembly: primary genome assembly GRCz11.104 http://ftp.ensembl.org/pub/release 104/fasta/danio rerio/dna/Danio rerio.GRCz11.dna sm.primary assembly.fa.gz and http://ftp.ensembl.org/pub/release 104/gtf/danio rerio/Danio rerio.GRCz11.104.gtf.gz Supplementary files format and content: The files with \" ReadsPerGenes.fastp.noD.tab\" name extensions are read counts per gene obtained from STAR  which were used in DESeq2 for differential expression analysis.", "1 dpf whole body embryos", "Two temperature protocols were used  either i a control constant temperature of 27\u00b0C  or ii  thermal stress protocol consisting of repeated heat stress with temperature fluctuations  between 27  29  32  29  and 27\u00b0C  with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium fresh medium free of metabolites or stress medium with stress metabolites  SM and incubated with their temperature protocols for 24 hours  from 11 am once they reached the stage of 2 3.3 hpf to 11 am on the next day. At 1 dpf  i.e. post 24 hours of experimental treatment  embryos were sampled by pools of 20 per condition  and snap frozen at  80\u00b0C before total RNA extraction.", "Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations  and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.", "Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish wild type AB maintained at 27\u00b0C  with 14:10 light:dark cycles.  Embryos were incubated in individual 0.2 mL PCR tubes one embryo per tube containing 200 \u03bcL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.", "tissue:1 dpf whole body embryos|genotype:Wild type Line: AB|time:1 dpf group:C|treatment:Control fresh medium at 27C", "GSM6806698", "GSM6806698: C2  sample RNA12; Danio rerio; RNA Seq", "GSM6806698 r1", "GSM6806698", "1", "Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations  and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP412040", null, "loader:fastq load.py", "211020_A00291_0393_AHM5V2DRXY_1_12030WK0009L01_1.fastq.gz 211020_A00291_0393_AHM5V2DRXY_1_12030WK0009L01_2.fastq.gz", "fastq fastq", 3600938900.0, 36009389.0, "GSM6806698 r1", "0:50 1:50", "A:947323197;C:850773040;G:856712191;T:946032751;N:97721", 50, 50, null, null, 947323197, 850773040, 856712191, 946032751, 97721, "SRX18540944", "SRS16005329", "SRA1555908", "Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull", "Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull", 2, 0.95605, 0.96282, 0.11507, 0.11791, 0.73667, 0.73738, 0.51713, 0.5174, 50, 50, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2022-12-08", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [72482, "SRR22577930", "SRX18540943", "SRS16005328", "SRP412040", "PRJNA910181", "Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos", "GSE220546", "Transcriptome Analysis", "Heat alters biology from molecular to ecological levels  but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here  we provide a comprehensive picture of the molecular signatures of this process  by integrating multiomic and phenotypic data. In individual zebrafish embryos  repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response  extracellular signalling  glycosaminoglycan/keratan sulphate  and lipid metabolism. Consequently  non heat exposed receivers exposed to stress metabolites only experienced accelerated catch up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most  mediated by apelin signalling. Our results prove the concept of indirect heat induced stress propagation towards naive receivers  inducing phenotypes comparable to those resulting from direct heat exposure  but utilising distinct molecular pathways. Group exposing a non laboratory zebrafish line  we independently confirm that the glycosaminoglycan biosynthesis related gene chs1  and the mucus glycoprotein gene prg4a  functionally connected to the candidate stress metabolite classes sugars and phosphocholine  are differentially expressed in receivers. This hints at the production of Schreckstoff like cues in receivers  leading to further stress propagation within groups  which may have ecological and animal welfare implications for aquatic populations in a changing climate. Overall design: Zebrafish embryos were exposed for 24 hours to thermal stress TS and stress metabolites SM released by heat stressed zebrafish embryos  in a two way factorial design TSxSM  yielding four experimental treatments: fresh medium at 27\u00b0C control C  fresh medium with thermal stress TS  medium containing stress metabolites at 27\u00b0C SM  and medium containing stress metabolites with thermal stress TS+SM. Each treatment contains n = 3 biological replicates  each representing the pooled gene expression from 20 individual embryos.", null, "pubmed:37228511", null, "SM2  sample RNA10", "GSM6806697", null, "source name:1 dpf whole body embryos|tissue:1 dpf whole body embryos|genotype:Wild type Line: AB|time:1 dpf group:SM|treatment:Stress Metabolites at 27C", "SM2  sample RNA10", "The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1. Reads were filtered and trimmed using fastp v0.23.1  to remove low quality reads  polyG  polyX  and Illumina adapter sequences. Default parameters were used along with   dup calc accuracy 3   trim poly g   trim poly x Reads were aligned to the zebrafish reference genome using STAR v2.6.1 Reads were counted by gene using STAR v2.6.1   runMode alignReads   quantMode TranscriptomeSAM GeneCounts   outSAMtype BAM SortedByCoordinate   outSAMunmapped None   outSAMattributes Standard Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2. Assembly: primary genome assembly GRCz11.104 http://ftp.ensembl.org/pub/release 104/fasta/danio rerio/dna/Danio rerio.GRCz11.dna sm.primary assembly.fa.gz and http://ftp.ensembl.org/pub/release 104/gtf/danio rerio/Danio rerio.GRCz11.104.gtf.gz Supplementary files format and content: The files with \" ReadsPerGenes.fastp.noD.tab\" name extensions are read counts per gene obtained from STAR  which were used in DESeq2 for differential expression analysis.", "1 dpf whole body embryos", "Two temperature protocols were used  either i a control constant temperature of 27\u00b0C  or ii  thermal stress protocol consisting of repeated heat stress with temperature fluctuations  between 27  29  32  29  and 27\u00b0C  with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium fresh medium free of metabolites or stress medium with stress metabolites  SM and incubated with their temperature protocols for 24 hours  from 11 am once they reached the stage of 2 3.3 hpf to 11 am on the next day. At 1 dpf  i.e. post 24 hours of experimental treatment  embryos were sampled by pools of 20 per condition  and snap frozen at  80\u00b0C before total RNA extraction.", "Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations  and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.", "Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish wild type AB maintained at 27\u00b0C  with 14:10 light:dark cycles.  Embryos were incubated in individual 0.2 mL PCR tubes one embryo per tube containing 200 \u03bcL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.", "tissue:1 dpf whole body embryos|genotype:Wild type Line: AB|time:1 dpf group:SM|treatment:Stress Metabolites at 27C", "GSM6806697", "GSM6806697: SM2  sample RNA10; Danio rerio; RNA Seq", "GSM6806697 r1", "GSM6806697", "1", "Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations  and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP412040", null, "loader:fastq load.py", "211020_A00291_0393_AHM5V2DRXY_1_12030WK0008L01_1.fastq.gz 211020_A00291_0393_AHM5V2DRXY_1_12030WK0008L01_2.fastq.gz", "fastq fastq", 2826043300.0, 28260433.0, "GSM6806697 r1", "0:50 1:50", "A:759619748;C:653720748;G:665257649;T:747369546;N:75609", 50, 50, null, null, 759619748, 653720748, 665257649, 747369546, 75609, "SRX18540943", "SRS16005328", "SRA1555908", "Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull", "Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull", 2, 0.95699, 0.9614, 0.09422, 0.09721, 0.73079, 0.73241, 0.48945, 0.49521, 50, 50, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2022-12-08", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [72483, "SRR22577931", "SRX18540942", "SRS16005327", "SRP412040", "PRJNA910181", "Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos", "GSE220546", "Transcriptome Analysis", "Heat alters biology from molecular to ecological levels  but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here  we provide a comprehensive picture of the molecular signatures of this process  by integrating multiomic and phenotypic data. In individual zebrafish embryos  repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response  extracellular signalling  glycosaminoglycan/keratan sulphate  and lipid metabolism. Consequently  non heat exposed receivers exposed to stress metabolites only experienced accelerated catch up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most  mediated by apelin signalling. Our results prove the concept of indirect heat induced stress propagation towards naive receivers  inducing phenotypes comparable to those resulting from direct heat exposure  but utilising distinct molecular pathways. Group exposing a non laboratory zebrafish line  we independently confirm that the glycosaminoglycan biosynthesis related gene chs1  and the mucus glycoprotein gene prg4a  functionally connected to the candidate stress metabolite classes sugars and phosphocholine  are differentially expressed in receivers. This hints at the production of Schreckstoff like cues in receivers  leading to further stress propagation within groups  which may have ecological and animal welfare implications for aquatic populations in a changing climate. Overall design: Zebrafish embryos were exposed for 24 hours to thermal stress TS and stress metabolites SM released by heat stressed zebrafish embryos  in a two way factorial design TSxSM  yielding four experimental treatments: fresh medium at 27\u00b0C control C  fresh medium with thermal stress TS  medium containing stress metabolites at 27\u00b0C SM  and medium containing stress metabolites with thermal stress TS+SM. Each treatment contains n = 3 biological replicates  each representing the pooled gene expression from 20 individual embryos.", null, "pubmed:37228511", null, "TS+SM2  sample RNA9", "GSM6806696", null, "source name:1 dpf whole body embryos|tissue:1 dpf whole body embryos|genotype:Wild type Line: AB|time:1 dpf group:TS+SM|treatment:Stress Metabolites with repeated heat stress", "TS+SM2  sample RNA9", "The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1. Reads were filtered and trimmed using fastp v0.23.1  to remove low quality reads  polyG  polyX  and Illumina adapter sequences. Default parameters were used along with   dup calc accuracy 3   trim poly g   trim poly x Reads were aligned to the zebrafish reference genome using STAR v2.6.1 Reads were counted by gene using STAR v2.6.1   runMode alignReads   quantMode TranscriptomeSAM GeneCounts   outSAMtype BAM SortedByCoordinate   outSAMunmapped None   outSAMattributes Standard Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2. Assembly: primary genome assembly GRCz11.104 http://ftp.ensembl.org/pub/release 104/fasta/danio rerio/dna/Danio rerio.GRCz11.dna sm.primary assembly.fa.gz and http://ftp.ensembl.org/pub/release 104/gtf/danio rerio/Danio rerio.GRCz11.104.gtf.gz Supplementary files format and content: The files with \" ReadsPerGenes.fastp.noD.tab\" name extensions are read counts per gene obtained from STAR  which were used in DESeq2 for differential expression analysis.", "1 dpf whole body embryos", "Two temperature protocols were used  either i a control constant temperature of 27\u00b0C  or ii  thermal stress protocol consisting of repeated heat stress with temperature fluctuations  between 27  29  32  29  and 27\u00b0C  with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium fresh medium free of metabolites or stress medium with stress metabolites  SM and incubated with their temperature protocols for 24 hours  from 11 am once they reached the stage of 2 3.3 hpf to 11 am on the next day. At 1 dpf  i.e. post 24 hours of experimental treatment  embryos were sampled by pools of 20 per condition  and snap frozen at  80\u00b0C before total RNA extraction.", "Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations  and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.", "Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish wild type AB maintained at 27\u00b0C  with 14:10 light:dark cycles.  Embryos were incubated in individual 0.2 mL PCR tubes one embryo per tube containing 200 \u03bcL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.", "tissue:1 dpf whole body embryos|genotype:Wild type Line: AB|time:1 dpf group:TS+SM|treatment:Stress Metabolites with repeated heat stress", "GSM6806696", "GSM6806696: TS+SM2  sample RNA9; Danio rerio; RNA Seq", "GSM6806696 r1", "GSM6806696", "1", "Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations  and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP412040", null, "loader:fastq load.py", "211020_A00291_0393_AHM5V2DRXY_1_12030WK0007L01_1.fastq.gz 211020_A00291_0393_AHM5V2DRXY_1_12030WK0007L01_2.fastq.gz", "fastq fastq", 3000657500.0, 30006575.0, "GSM6806696 r1", "0:50 1:50", "A:796059736;C:686227472;G:732263299;T:786033681;N:73312", 50, 50, null, null, 796059736, 686227472, 732263299, 786033681, 73312, "SRX18540942", "SRS16005327", "SRA1555908", "Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull", "Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull", 2, 0.95934, 0.96295, 0.08991, 0.09091, 0.74462, 0.74424, 0.48055, 0.49465, 50, 50, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2022-12-08", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [72484, "SRR22577932", "SRX18540941", "SRS16005326", "SRP412040", "PRJNA910181", "Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos", "GSE220546", "Transcriptome Analysis", "Heat alters biology from molecular to ecological levels  but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here  we provide a comprehensive picture of the molecular signatures of this process  by integrating multiomic and phenotypic data. In individual zebrafish embryos  repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response  extracellular signalling  glycosaminoglycan/keratan sulphate  and lipid metabolism. Consequently  non heat exposed receivers exposed to stress metabolites only experienced accelerated catch up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most  mediated by apelin signalling. Our results prove the concept of indirect heat induced stress propagation towards naive receivers  inducing phenotypes comparable to those resulting from direct heat exposure  but utilising distinct molecular pathways. Group exposing a non laboratory zebrafish line  we independently confirm that the glycosaminoglycan biosynthesis related gene chs1  and the mucus glycoprotein gene prg4a  functionally connected to the candidate stress metabolite classes sugars and phosphocholine  are differentially expressed in receivers. This hints at the production of Schreckstoff like cues in receivers  leading to further stress propagation within groups  which may have ecological and animal welfare implications for aquatic populations in a changing climate. Overall design: Zebrafish embryos were exposed for 24 hours to thermal stress TS and stress metabolites SM released by heat stressed zebrafish embryos  in a two way factorial design TSxSM  yielding four experimental treatments: fresh medium at 27\u00b0C control C  fresh medium with thermal stress TS  medium containing stress metabolites at 27\u00b0C SM  and medium containing stress metabolites with thermal stress TS+SM. Each treatment contains n = 3 biological replicates  each representing the pooled gene expression from 20 individual embryos.", null, "pubmed:37228511", null, "TS2  sample RNA7", "GSM6806695", null, "source name:1 dpf whole body embryos|tissue:1 dpf whole body embryos|genotype:Wild type Line: AB|time:1 dpf group:TS|treatment:Fresh medium with repeated heat stress", "TS2  sample RNA7", "The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1. Reads were filtered and trimmed using fastp v0.23.1  to remove low quality reads  polyG  polyX  and Illumina adapter sequences. Default parameters were used along with   dup calc accuracy 3   trim poly g   trim poly x Reads were aligned to the zebrafish reference genome using STAR v2.6.1 Reads were counted by gene using STAR v2.6.1   runMode alignReads   quantMode TranscriptomeSAM GeneCounts   outSAMtype BAM SortedByCoordinate   outSAMunmapped None   outSAMattributes Standard Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2. Assembly: primary genome assembly GRCz11.104 http://ftp.ensembl.org/pub/release 104/fasta/danio rerio/dna/Danio rerio.GRCz11.dna sm.primary assembly.fa.gz and http://ftp.ensembl.org/pub/release 104/gtf/danio rerio/Danio rerio.GRCz11.104.gtf.gz Supplementary files format and content: The files with \" ReadsPerGenes.fastp.noD.tab\" name extensions are read counts per gene obtained from STAR  which were used in DESeq2 for differential expression analysis.", "1 dpf whole body embryos", "Two temperature protocols were used  either i a control constant temperature of 27\u00b0C  or ii  thermal stress protocol consisting of repeated heat stress with temperature fluctuations  between 27  29  32  29  and 27\u00b0C  with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium fresh medium free of metabolites or stress medium with stress metabolites  SM and incubated with their temperature protocols for 24 hours  from 11 am once they reached the stage of 2 3.3 hpf to 11 am on the next day. At 1 dpf  i.e. post 24 hours of experimental treatment  embryos were sampled by pools of 20 per condition  and snap frozen at  80\u00b0C before total RNA extraction.", "Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations  and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.", "Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish wild type AB maintained at 27\u00b0C  with 14:10 light:dark cycles.  Embryos were incubated in individual 0.2 mL PCR tubes one embryo per tube containing 200 \u03bcL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.", "tissue:1 dpf whole body embryos|genotype:Wild type Line: AB|time:1 dpf group:TS|treatment:Fresh medium with repeated heat stress", "GSM6806695", "GSM6806695: TS2  sample RNA7; Danio rerio; RNA Seq", "GSM6806695 r1", "GSM6806695", "1", "Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations  and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP412040", null, "loader:fastq load.py", "211020_A00291_0393_AHM5V2DRXY_1_12030WK0005L01_1.fastq.gz 211020_A00291_0393_AHM5V2DRXY_1_12030WK0005L01_2.fastq.gz", "fastq fastq", 2782782000.0, 27827820.0, "GSM6806695 r1", "0:50 1:50", "A:748478002;C:640727379;G:651947739;T:741552359;N:76521", 50, 50, null, null, 748478002, 640727379, 651947739, 741552359, 76521, "SRX18540941", "SRS16005326", "SRA1555908", "Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull", "Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull", 2, 0.95766, 0.96118, 0.08698, 0.08838, 0.74231, 0.74282, 0.49457, 0.48485, 50, 50, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2022-12-08", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [72485, "SRR22577934", "SRX18540940", "SRS16005325", "SRP412040", "PRJNA910181", "Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos", "GSE220546", "Transcriptome Analysis", "Heat alters biology from molecular to ecological levels  but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here  we provide a comprehensive picture of the molecular signatures of this process  by integrating multiomic and phenotypic data. In individual zebrafish embryos  repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response  extracellular signalling  glycosaminoglycan/keratan sulphate  and lipid metabolism. Consequently  non heat exposed receivers exposed to stress metabolites only experienced accelerated catch up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most  mediated by apelin signalling. Our results prove the concept of indirect heat induced stress propagation towards naive receivers  inducing phenotypes comparable to those resulting from direct heat exposure  but utilising distinct molecular pathways. Group exposing a non laboratory zebrafish line  we independently confirm that the glycosaminoglycan biosynthesis related gene chs1  and the mucus glycoprotein gene prg4a  functionally connected to the candidate stress metabolite classes sugars and phosphocholine  are differentially expressed in receivers. This hints at the production of Schreckstoff like cues in receivers  leading to further stress propagation within groups  which may have ecological and animal welfare implications for aquatic populations in a changing climate. Overall design: Zebrafish embryos were exposed for 24 hours to thermal stress TS and stress metabolites SM released by heat stressed zebrafish embryos  in a two way factorial design TSxSM  yielding four experimental treatments: fresh medium at 27\u00b0C control C  fresh medium with thermal stress TS  medium containing stress metabolites at 27\u00b0C SM  and medium containing stress metabolites with thermal stress TS+SM. Each treatment contains n = 3 biological replicates  each representing the pooled gene expression from 20 individual embryos.", null, "pubmed:37228511", null, "TS1  sample RNA6", "GSM6806694", null, "source name:1 dpf whole body embryos|tissue:1 dpf whole body embryos|genotype:Wild type Line: AB|time:1 dpf group:TS|treatment:Fresh medium with repeated heat stress", "TS1  sample RNA6", "The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1. Reads were filtered and trimmed using fastp v0.23.1  to remove low quality reads  polyG  polyX  and Illumina adapter sequences. Default parameters were used along with   dup calc accuracy 3   trim poly g   trim poly x Reads were aligned to the zebrafish reference genome using STAR v2.6.1 Reads were counted by gene using STAR v2.6.1   runMode alignReads   quantMode TranscriptomeSAM GeneCounts   outSAMtype BAM SortedByCoordinate   outSAMunmapped None   outSAMattributes Standard Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2. Assembly: primary genome assembly GRCz11.104 http://ftp.ensembl.org/pub/release 104/fasta/danio rerio/dna/Danio rerio.GRCz11.dna sm.primary assembly.fa.gz and http://ftp.ensembl.org/pub/release 104/gtf/danio rerio/Danio rerio.GRCz11.104.gtf.gz Supplementary files format and content: The files with \" ReadsPerGenes.fastp.noD.tab\" name extensions are read counts per gene obtained from STAR  which were used in DESeq2 for differential expression analysis.", "1 dpf whole body embryos", "Two temperature protocols were used  either i a control constant temperature of 27\u00b0C  or ii  thermal stress protocol consisting of repeated heat stress with temperature fluctuations  between 27  29  32  29  and 27\u00b0C  with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium fresh medium free of metabolites or stress medium with stress metabolites  SM and incubated with their temperature protocols for 24 hours  from 11 am once they reached the stage of 2 3.3 hpf to 11 am on the next day. At 1 dpf  i.e. post 24 hours of experimental treatment  embryos were sampled by pools of 20 per condition  and snap frozen at  80\u00b0C before total RNA extraction.", "Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations  and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.", "Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish wild type AB maintained at 27\u00b0C  with 14:10 light:dark cycles.  Embryos were incubated in individual 0.2 mL PCR tubes one embryo per tube containing 200 \u03bcL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.", "tissue:1 dpf whole body embryos|genotype:Wild type Line: AB|time:1 dpf group:TS|treatment:Fresh medium with repeated heat stress", "GSM6806694", "GSM6806694: TS1  sample RNA6; Danio rerio; RNA Seq", "GSM6806694 r1", "GSM6806694", "1", "Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations  and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP412040", null, "loader:fastq load.py", "211020_A00291_0393_AHM5V2DRXY_1_12030WK0004L01_1.fastq.gz 211020_A00291_0393_AHM5V2DRXY_1_12030WK0004L01_2.fastq.gz", "fastq fastq", 3939313200.0, 39393132.0, "GSM6806694 r1", "0:50 1:50", "A:1060730800;C:904303497;G:928318245;T:1045853002;N:107656", 50, 50, null, null, 1060730800, 904303497, 928318245, 1045853002, 107656, "SRX18540940", "SRS16005325", "SRA1555908", "Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull", "Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull", 2, 0.95569, 0.96038, 0.08993, 0.09123, 0.74377, 0.74446, 0.46546, 0.49016, 50, 50, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2022-12-08", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"], [72486, "SRR22577935", "SRX18540939", "SRS16005324", "SRP412040", "PRJNA910181", "Transcriptomic data for: Heat induces multiomic and phenotypic stress propagation in zebrafish embryos", "GSE220546", "Transcriptome Analysis", "Heat alters biology from molecular to ecological levels  but may also have unknown indirect effects. This includes the concept that animals exposed to abiotic stress can induce stress in naive receivers. Here  we provide a comprehensive picture of the molecular signatures of this process  by integrating multiomic and phenotypic data. In individual zebrafish embryos  repeated heat peaks elicited both a molecular response and a burst of accelerated growth followed by a growth slow down in concert with reduced responses to novel stimuli. Metabolomes of the media of heat treated vs. untreated embryos revealed candidate stress metabolites including sulphur containing compounds and lipids. These stress metabolites elicited transcriptomic changes in naive receivers related to immune response  extracellular signalling  glycosaminoglycan/keratan sulphate  and lipid metabolism. Consequently  non heat exposed receivers exposed to stress metabolites only experienced accelerated catch up growth in concert with reduced swimming performance. The combination of heat and stress metabolites accelerated development the most  mediated by apelin signalling. Our results prove the concept of indirect heat induced stress propagation towards naive receivers  inducing phenotypes comparable to those resulting from direct heat exposure  but utilising distinct molecular pathways. Group exposing a non laboratory zebrafish line  we independently confirm that the glycosaminoglycan biosynthesis related gene chs1  and the mucus glycoprotein gene prg4a  functionally connected to the candidate stress metabolite classes sugars and phosphocholine  are differentially expressed in receivers. This hints at the production of Schreckstoff like cues in receivers  leading to further stress propagation within groups  which may have ecological and animal welfare implications for aquatic populations in a changing climate. Overall design: Zebrafish embryos were exposed for 24 hours to thermal stress TS and stress metabolites SM released by heat stressed zebrafish embryos  in a two way factorial design TSxSM  yielding four experimental treatments: fresh medium at 27\u00b0C control C  fresh medium with thermal stress TS  medium containing stress metabolites at 27\u00b0C SM  and medium containing stress metabolites with thermal stress TS+SM. Each treatment contains n = 3 biological replicates  each representing the pooled gene expression from 20 individual embryos.", null, "pubmed:37228511", null, "TS+SM1  sample RNA5", "GSM6806693", null, "source name:1 dpf whole body embryos|tissue:1 dpf whole body embryos|genotype:Wild type Line: AB|time:1 dpf group:TS+SM|treatment:Stress Metabolites with repeated heat stress", "TS+SM1  sample RNA5", "The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1. Reads were filtered and trimmed using fastp v0.23.1  to remove low quality reads  polyG  polyX  and Illumina adapter sequences. Default parameters were used along with   dup calc accuracy 3   trim poly g   trim poly x Reads were aligned to the zebrafish reference genome using STAR v2.6.1 Reads were counted by gene using STAR v2.6.1   runMode alignReads   quantMode TranscriptomeSAM GeneCounts   outSAMtype BAM SortedByCoordinate   outSAMunmapped None   outSAMattributes Standard Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2. Assembly: primary genome assembly GRCz11.104 http://ftp.ensembl.org/pub/release 104/fasta/danio rerio/dna/Danio rerio.GRCz11.dna sm.primary assembly.fa.gz and http://ftp.ensembl.org/pub/release 104/gtf/danio rerio/Danio rerio.GRCz11.104.gtf.gz Supplementary files format and content: The files with \" ReadsPerGenes.fastp.noD.tab\" name extensions are read counts per gene obtained from STAR  which were used in DESeq2 for differential expression analysis.", "1 dpf whole body embryos", "Two temperature protocols were used  either i a control constant temperature of 27\u00b0C  or ii  thermal stress protocol consisting of repeated heat stress with temperature fluctuations  between 27  29  32  29  and 27\u00b0C  with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium fresh medium free of metabolites or stress medium with stress metabolites  SM and incubated with their temperature protocols for 24 hours  from 11 am once they reached the stage of 2 3.3 hpf to 11 am on the next day. At 1 dpf  i.e. post 24 hours of experimental treatment  embryos were sampled by pools of 20 per condition  and snap frozen at  80\u00b0C before total RNA extraction.", "Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations  and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.", "Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish wild type AB maintained at 27\u00b0C  with 14:10 light:dark cycles.  Embryos were incubated in individual 0.2 mL PCR tubes one embryo per tube containing 200 \u03bcL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.", "tissue:1 dpf whole body embryos|genotype:Wild type Line: AB|time:1 dpf group:TS+SM|treatment:Stress Metabolites with repeated heat stress", "GSM6806693", "GSM6806693: TS+SM1  sample RNA5; Danio rerio; RNA Seq", "GSM6806693 r1", "GSM6806693", "1", "Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations  and followed by a DNAse I digestion step and a sodium acetate clean up. Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP412040", null, "loader:fastq load.py", "211020_A00291_0393_AHM5V2DRXY_2_12030WK0003L01_1.fastq.gz 211020_A00291_0393_AHM5V2DRXY_2_12030WK0003L01_2.fastq.gz", "fastq fastq", 8000459900.0, 80004599.0, "GSM6806693 r1", "0:50 1:50", "A:2083773111;C:1806672672;G:2034786557;T:2075008672;N:218888", 50, 50, null, null, 2083773111, 1806672672, 2034786557, 2075008672, 218888, "SRX18540939", "SRS16005324", "SRA1555908", "Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull", "Odysyslab/MolStressH2O, Biological and Marine Sciences, University of Hull", 2, 0.9561, 0.96287, 0.07306, 0.08163, 0.76361, 0.76329, 0.48922, 0.48488, 50, 50, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "United Kingdom", "2022-12-08", "Multi-stage", "Multi-stage", "Trunk", "Surface Structure"]], "truncated": false, "filtered_table_rows_count": 116, "expanded_columns": [], "expandable_columns": [], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": [], "units": {}, "query": {"sql": "select rowid, [run.accession], [experiment.accession], [sample.accession], [study.accession], bioproject, [study.title], [study.alias], [study.type], [study.abstract], [study.attributes], [study.PMIDs], [sample.description], [sample.title], [sample.alias], [sample.centername], [sample.attributes], [GEOsample.title], [GEOsample.dataprocessing], [GEOsample.source], [GEOsample.treatmentprotocol], [GEOsample.extractprotocol], [GEOsample.growthprotocol], [GEOsample.characteristics], [GEOsample.accession], [experiment.title], [experiment.alias], [experiment.library_name], [experiment.design_description], [experiment.library_construction_protocol], [experiment.attributes], [experiment.library_strategy], [experiment.library_source], [experiment.library_selection], [experiment.library_layout], [experiment.platform], [experiment.instrument_model], [experiment.spot_descriptor], [experiment.study_ref], [run.title], [run.attributes], [run.filename], [run.semantic_name], [run.total_bases], [run.total_spots], [run.alias], [run.read_lengths], [run.base_counts], [run.r1_length], [run.r2_length], [run.r3_length], [run.r4_length], [run.Acount], [run.Ccount], [run.Gcount], [run.Tcount], [run.Ncount], [run.experiment], [run.pool_member], [submission.accession], [submission.srasource], [submission.bioprojectsource], [seqdetective.n_mates], [seqdetective.mapping_rate.mate1], [seqdetective.mapping_rate.mate2], [seqdetective.nofeature_rate.mate1], [seqdetective.nofeature_rate.mate2], [seqdetective.sparsity.mate1], [seqdetective.sparsity.mate2], [seqdetective.pos_strand_rate.mate1], [seqdetective.pos_strand_rate.mate2], [seqdetective.readlen.mate1], [seqdetective.readlen.mate2], [seqdetective.judgement.mate1], [seqdetective.judgement.mate2], [seqdetective.judgement.reason], platform_family, instrument_generation, read_bias, selection_class, prep_kit, sc_or_bulk, tech_class, technology, tech_variant, [submission.bioprojectsource.country], earliest_date, devstage_curation, devstage_curation_coarse, tissue_curation, tissue_curation_coarse from run_metadata where \"devstage_curation_coarse\" = :p0 and \"tissue_curation\" = :p1 order by rowid limit 101", "params": {"p0": "Multi-stage", "p1": "Trunk"}}, "facet_results": {"experiment.library_strategy": {"name": "experiment.library_strategy", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk", "results": [{"value": "RNA-Seq", "label": "RNA-Seq", "count": 92, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk&experiment.library_strategy=RNA-Seq", "selected": false}, {"value": "WGS", "label": "WGS", "count": 24, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk&experiment.library_strategy=WGS", "selected": false}], "truncated": false}, "experiment.library_source": {"name": "experiment.library_source", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk", "results": [{"value": "TRANSCRIPTOMIC", "label": "TRANSCRIPTOMIC", "count": 116, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk&experiment.library_source=TRANSCRIPTOMIC", "selected": false}], "truncated": false}, "experiment.library_selection": {"name": "experiment.library_selection", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk", "results": [{"value": "cDNA", "label": "cDNA", "count": 77, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk&experiment.library_selection=cDNA", "selected": false}, {"value": "RANDOM", "label": "RANDOM", "count": 24, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk&experiment.library_selection=RANDOM", "selected": false}, {"value": "PolyA", "label": "PolyA", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk&experiment.library_selection=PolyA", "selected": false}, {"value": "Oligo-dT", "label": "Oligo-dT", "count": 6, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk&experiment.library_selection=Oligo-dT", "selected": false}], "truncated": false}, "experiment.library_layout": {"name": "experiment.library_layout", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk", "results": [{"value": "PAIRED", "label": "PAIRED", "count": 90, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk&experiment.library_layout=PAIRED", "selected": false}, {"value": "SINGLE", "label": "SINGLE", "count": 26, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk&experiment.library_layout=SINGLE", "selected": false}], "truncated": false}, "experiment.platform": {"name": "experiment.platform", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk", "results": [{"value": "ILLUMINA", "label": "ILLUMINA", "count": 77, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk&experiment.platform=ILLUMINA", "selected": false}, {"value": "BGISEQ", "label": "BGISEQ", "count": 30, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk&experiment.platform=BGISEQ", "selected": false}, {"value": "DNBSEQ", "label": "DNBSEQ", "count": 9, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk&experiment.platform=DNBSEQ", "selected": false}], "truncated": false}, "devstage_curation_coarse": {"name": "devstage_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk", "results": [{"value": "Multi-stage", "label": "Multi-stage", "count": 116, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?tissue_curation=Trunk", "selected": true}], "truncated": false}, "devstage_curation": {"name": "devstage_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk", "results": [{"value": "Multi-stage", "label": "Multi-stage", "count": 92, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk&devstage_curation=Multi-stage", "selected": false}, {"value": "Undetermined", "label": "Undetermined", "count": 24, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk&devstage_curation=Undetermined", "selected": false}], "truncated": false}, "tissue_curation_coarse": {"name": "tissue_curation_coarse", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk", "results": [{"value": "Surface Structure", "label": "Surface Structure", "count": 116, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk&tissue_curation_coarse=Surface+Structure", "selected": false}], "truncated": false}, "tissue_curation": {"name": "tissue_curation", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk", "results": [{"value": "Trunk", "label": "Trunk", "count": 116, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage", "selected": true}], "truncated": false}, "technology": {"name": "technology", "type": "column", "hideable": false, "toggle_url": "/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk", "results": [{"value": "unknown", "label": "unknown", "count": 96, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk&technology=unknown", "selected": false}, {"value": "bulk", "label": "bulk", "count": 18, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk&technology=bulk", "selected": false}, {"value": "10x", "label": "10x", "count": 2, "toggle_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk&technology=10x", "selected": false}], "truncated": false}}, "suggested_facets": [], "next": "72486", "next_url": "http://metadata.rnaquarium.org/metadata/run_metadata.json?devstage_curation_coarse=Multi-stage&tissue_curation=Trunk&_next=72486", "private": false, "allow_execute_sql": true, "query_ms": 94.46872999251354}